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Fan, Xiao-Yan, Jing-Feng Gao, Kai-Ling Pan, Ding-Chang Li, and Hui-Hui Dai. "Temporal dynamics of bacterial communities and predicted nitrogen metabolism genes in a full-scale wastewater treatment plant." RSC Advances 7, no. 89 (2017): 56317–27. http://dx.doi.org/10.1039/c7ra10704h.
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Kanji, Farhaan, Himanshi Khurana, Caitlin Sherry, and Evangeline Ng. "A simulated metagenomic analysis of the gut microbiota of Anorexia Nervosa patients using PICRUSt." STEM Fellowship Journal 3, no. 2 (December 1, 2017): 1–3. http://dx.doi.org/10.17975/sfj-2017-012.
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Introduction Mack et al. (2016) studied the fecal bacteria and archaea of 55 European normal-weight participants (NW), 55 European patients with anorexia nervosa (ANT1), and 44 ANT1 patients following a body mass index increase (ANT2). Spreadsheets of identified microbes and their relative abundance per patient were uploaded to the EBI Metagenomics web server by Mack et al. We aimed to further study the functions of the identified microbes using the PICUSt algorithm (Langille, 2013) and see if these functions are consistent with published literature. Methods Spreadsheets were downloaded from EBI Metagenomics (Project# ERP012549) in JSON Biom format and uploaded to a Galaxy cloud server hosting PICRUSt. All data transformations can be viewed at http://huttenhower.sph.harvard.edu/galaxy/u/farhaansgroup/h/anorexi-astem-2017 . Transformed datasets were downloaded, appended with a .biom file extension, converted to the SPF format using STAMP v2.1.3 (Parks, 2014), and merged into a single file using Microsoft Excel for analysis with STAMP. Differences in propionate metabolism between ANT1, ANT2, and NW samples was chosen for further study. Results & Discussion The proportion of propionate metabolism genes was not significantly different between ANT1 and NW samples (p=0.08), but was different between ANT2 and NW samples (p=0.01) using a pair-wise Welsh’s t-test (0.95 CI) with a Storey FDR multiple test correction. In comparison, Mack et al, detected no differences in propionate concentration between AN and NW fecal samples using gas chromatography while Morito et al (2015) found lower concentrations of propionate in Japanese AN versus NW fecal samples using liquid chromatography. Our discrepancy with Mack et al could have arisen since PICRUSt cannot analyze the genes of eukaryotes, PICRUSt is limited by the depth and breadth of the gene annotations in the KEGG database, and our experimental setup cannot provide data on gene expression. Moreover, 18% of V4 16S rRNA DNA sequences could not be matched to any bacteria or archaea by EBI Metagenomics. In conclusion, while in silico experiments can be useful to predict microbial functions in a sample, in this case, our PICRUSt-based hypothesis that fecal samples from Mack et al would have different concentrations of propionate between AN and NW samples was not borne out by Mack et al’s chromatography experiments. Nonetheless, the conflicting findings between us, Mack et al, and Morito et al warrants further research on whether microbes mediate carbohydrate metabolism differently in patients with a history of anorexia nervosa versus controls.
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LeBrun, Erick S., and Sanghoon Kang. "A comparison of computationally predicted functional metagenomes and microarray analysis for microbial P cycle genes in a unique basalt-soil forest." F1000Research 7 (February 12, 2018): 179. http://dx.doi.org/10.12688/f1000research.13841.1.
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Here we compared microbial results for the same Phosphorus (P) biogeochemical cycle genes from a GeoChip microarray and PICRUSt functional predictions from 16S rRNA data for 20 samples in the four spatially separated Gotjawal forests on Jeju Island in South Korea. The high homogeneity of microbial communities detected at each site allows sites to act as environmental replicates for comparing the two different functional analysis methods. We found that while both methods capture the homogeneity of the system, both differed greatly in the total abundance of genes detected, as well as the diversity of taxa detected. Additionally, we introduce a more comprehensive functional assay that again captures the homogeneity of the system but also captures more extensive community gene and taxonomic information and depth. While both methods have their advantages and limitations, PICRUSt appears better suited to asking questions specifically related to microbial community P as we did here. This comparison of methods makes important distinctions between both the results and the capabilities of each method and can help select the best tool for answering different scientific questions.
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Agrawal, Shelesh, Co Thi Kinh, Thomas Schwartz, Masaaki Hosomi, Akihiko Terada, and Susanne Lackner. "Determining uncertainties in PICRUSt analysis – An easy approach for autotrophic nitrogen removal." Biochemical Engineering Journal 152 (December 2019): 107328. http://dx.doi.org/10.1016/j.bej.2019.107328.
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Luo, Yiting, Fangyuan Zhu, Jiaqian Wu, Jin Wu, Pei Wu, and Yingchao Liu. "Effect of Shenling Baizhu San on Intestinal Flora in a Rat Model of Ulcerative Colitis with Spleen Deficiency and Dampness." Evidence-Based Complementary and Alternative Medicine 2022 (February 12, 2022): 1–24. http://dx.doi.org/10.1155/2022/9985147.
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Objective. Shenling Baizhu San (SLBZS) is reported as an effective drug for ulcerative colitis (UC); however, its effect on intestinal flora remains unknown. In this study, we investigated the effect of SLBZS on intestinal flora in a rat model of UC with spleen deficiency and dampness. Methods. UC was induced in rats using 2,4,6-trinitrobenzene sulfonic acid on the basis of a model of spleen deficiency and dampness. The 16S rDNA sequencing was used to detect structural changes in the intestinal flora; the phylogenetic investigation of communities by reconstruction of unobserved state (PICRUSt) analysis was used to predict the altered pathways. Results. Compared with the model group, rats in the SLBZS group exhibited decreased levels of TNF-α P < 0.05 , and increased abundance and diversity of the intestinal flora. The abundance of Actinobacteria P < 0.001 and Bacteroides P < 0.01 increased and that of Firmicutes decreased P < 0.001 , and the abundance of Bifidobacterium P < 0.05 and Allobaculum increased. PICRUSt analysis showed that the altered pathways between the groups were those of fatty acid and antibiotic biosynthesis, amino acid metabolism, and the pentose phosphate pathway. Conclusions. SLBZS can regulate the structure and function of the intestinal flora, alter expression levels of certain metabolic pathways, and has the potential to treat UC.
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Yin, Yanan, and Jianlong Wang. "Predictive functional profiling of microbial communities in fermentative hydrogen production system using PICRUSt." International Journal of Hydrogen Energy 46, no. 5 (January 2021): 3716–25. http://dx.doi.org/10.1016/j.ijhydene.2020.10.246.
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Xu, Letian, Liuwei Sun, Shihan Zhang, Shanshan Wang, and Min Lu. "High-Resolution Profiling of Gut Bacterial Communities in an Invasive Beetle using PacBio SMRT Sequencing System." Insects 10, no. 8 (August 14, 2019): 248. http://dx.doi.org/10.3390/insects10080248.
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Dendroctonus valens, an invasive bark beetle, has caused severe damage to Chinese forests. Previous studies have highlighted the importance of the gut microbiota and its fundamental role in host fitness. Culture-dependent and culture-independent methods have been applied in analyzing beetles’ gut microbiota. The former method cannot present a whole picture of the community, and the latter mostly generates short read lengths that cannot be assigned to species. Here, the PacBio sequencing system was utilized to capture full-length 16S rRNA sequences in D. valens gut throughout its ontogeny. A total of eight phyla, 55 families, 102 genera, and 253 species were identified. Bacterial communities in colonized beetles have the greatest richness but the lowest evenness in all life stages, which is different from those in young larvae. Pseudomonas sp., Serratia liquefaciens possess high abundance throughout its ontogeny and may serve as members of the core bacteriome. A phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis predicted that gut microbiota in larvae are rich in genes involved in carbohydrate, energy metabolism. Gut microbiota in both larvae and colonized beetles are rich in xenobiotics and terpenoids biodegradation, which are decreased in dispersal beetles. Considering that the results are based mainly on the analysis of 16S rRNA sequencing and PICRUSt prediction, further confirmation is needed to improve the knowledge of the gut microbiota in D. valens and help to resolve taxonomic uncertainty at the species level.
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Gressel, Gregory M., Mykhaylo Usyk, Marina Frimer, D. Y. S. Kuo, and Robert D. Burk. "Characterization of the endometrial, cervicovaginal and anorectal microbiota in post-menopausal women with endometrioid and serous endometrial cancers." PLOS ONE 16, no. 11 (November 5, 2021): e0259188. http://dx.doi.org/10.1371/journal.pone.0259188.
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Objective To characterize the microbiota of postmenopausal women undergoing hysterectomy for endometrioid (EAC) or uterine serous cancers (USC) compared to controls with non-malignant conditions. Methods Endometrial, cervicovaginal and anorectal microbial swabs were obtained from 35 postmenopausal women (10 controls, 14 EAC and 11 USC) undergoing hysterectomy. Extracted DNA was PCR amplified using barcoded 16S rRNA gene V4 primers. Sequenced libraries were processed using QIIME2. Phyloseq was used to calculate α- and β- diversity measures. Biomarkers associated with case status were identified using ANCOM after adjustment for patient age, race and BMI. PICRUSt was used to identify microbial pathways associated with case status. Results Beta-diversity of microbial communities across each niche was significantly different (R2 = 0.25, p < 0.001). Alpha-diversity of the uterine microbiome was reduced in USC (Chao1, p = 0.004 and Fisher, p = 0.007) compared to EAC. Biomarkers from the three anatomical sites allowed samples to be clustered into two distinct clades that distinguished controls from USC cases (p = 0.042). The USC group was defined by 13 bacterial taxa across the three sites (W-stat>10, FDR<0.05) including depletion of cervicovaginal Lactobacillus and elevation of uterine Pseudomonas. PICRUSTt analysis revealed highly significant differences between the USC-associated clades within the cervicovaginal and uterine microbiota. Conclusions The microbial diversity of anatomic niches in postmenopausal women with EAC and USC is different compared to controls. Multiple bacteria are associated with USC case status including elevated levels of cervicovaginal Lactobacillus, depletion of uterine Pseudomonas, and substantially different functional potentials identified within cervicovaginal and uterine niches.
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Li, Yao, Hai-Fang Wang, Xin Li, Hai-Xia Li, Qiong Zhang, Hong-Wei Zhou, Yan He, et al. "Disordered intestinal microbes are associated with the activity of Systemic Lupus Erythematosus." Clinical Science 133, no. 7 (April 2019): 821–38. http://dx.doi.org/10.1042/cs20180841.
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Abstract Intestinal dysbiosis is implicated in Systemic Lupus Erythematosus (SLE). However, the evidence of gut microbiome changes in SLE is limited, and the association of changed gut microbiome with the activity of SLE, as well as its functional relevance with SLE still remains unknown. Here, we sequenced 16S rRNA amplicon on fecal samples from 40 SLE patients (19 active patients, 21 remissive patients), 20 disease controls (Rheumatoid Arthritis (RA) patients), and 22 healthy controls (HCs), and investigated the association of functional categories with taxonomic composition by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). We demonstrated SLE patients, particularly the active patients, had significant dysbiosis in gut microbiota with reduced bacterial diversity and biased community constitutions. Amongst the disordered microbiota, the genera Streptococcus, Campylobacter, Veillonella, the species anginosus and dispar, were positively correlated with lupus activity, while the genus Bifidobacterium was negatively associated with the disease activity. PICRUSt analysis showed metabolic pathways were different between SLE and HCs, and also between active and remissive SLE patients. Moreover, we revealed that a random forest model could distinguish SLE from RA and HCs (area under the curve (AUC) = 0.792), and another random forest model could well predict the activity of SLE patients (AUC = 0.811). In summary, SLE patients, especially the active patients, show an apparent dysbiosis in gut microbiota and its related metabolic pathways. Amongst the disordered microflora, four genera and two species are associated with lupus activity. Furthermore, the random forest models are able to diagnose SLE and predict disease activity.
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Kuballa, Anna, Marco Geraci, Meredith Johnston, and Dario Sorrentino. "The Gut Microbial Profile of Preclinical Crohn’s Disease Is Similar to That of Healthy Controls." Inflammatory Bowel Diseases 26, no. 11 (April 27, 2020): 1682–90. http://dx.doi.org/10.1093/ibd/izaa072.
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Abstract Background and Aims It is unclear whether microbial dysbiosis plays an etiologic role in Crohn’s disease (CD) or is the result of protracted inflammation. Here, we test the hypothesis that dysbiosis predates clinical CD in asymptomatic first-degree relatives (FDRs) of CD patients: normal (FDR1), with borderline inflammation (FDR2), and with frank, very early inflammation (FDR3). Methods The gut microbial diversity was tested in ileocecal biopsies through next generation sequencing of the 16S rRNA gene in 10 healthy controls (HCs), 22 patients with active, untreated CD, and 25 FDRs (9 FDR1; 12 FDR2; 4 FDR3). The metagenomic functions of 41 microbiome-related processes were inferred by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis. Results Compared with HCs, alpha diversity in CD patients was decreased, with an observed decrease in Faecalibacterium prausnitzii and increase in Bacteroides fragilis. In FDRs, microbial diversity was unchanged compared with HCs. In Operational Taxonomic Units and PICRUSt Principal coordinates and component analyses, the ellipse centroid of FDRs was diagonally opposed to that of CD patients, but close to the HC centroid. In both analyses, statistically significant differences in terms of beta diversity were found between CD and HC but not between FDR and HC. Conclusions In FDRs (including FDR3—who bear preclinical/biologic onset disease), we found that the microbial profile is remarkably similar to HC. If confirmed in larger studies, this finding suggests that clinical CD-associated dysbiosis could result from the changed microenvironment due to disease evolution over time.
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Tong, Wenjie, Junying Li, Wenfeng Cong, Cuiping Zhang, Zhaoli Xu, Xiaolong Chen, Min Yang, Jiani Liu, Lei Yu, and Xiaopeng Deng. "Bacterial Community Structure and Function Shift in Rhizosphere Soil of Tobacco Plants Infected by Meloidogyne incognita." Plant Pathology Journal 38, no. 6 (December 1, 2022): 583–92. http://dx.doi.org/10.5423/ppj.oa.08.2022.0105.
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Root-knot nematode disease is a widespread and catastrophic disease of tobacco. However, little is known about the relationship between rhizosphere bacterial community and root-knot nematode disease. This study used 16S rRNA gene sequencing and PICRUSt to assess bacterial community structure and function changes in rhizosphere soil from <i>Meloidogyne incognita</i>-infected tobacco plants. We studied the rhizosphere bacterial community structure of <i>M. incognita</i>-infected and uninfected tobacco plants through a paired comparison design in two regions of tobacco planting area, Yuxi and Jiuxiang of Yunnan Province, southwest China. According to the findings, <i>M. incognita</i> infection can alter the bacterial population in the soil. Uninfested soil has more operational taxonomic unit numbers and richness than infested soil. Principal Coordinate Analysis revealed clear separations between bacterial communities from infested and uninfested soil, indicating that different infection conditions resulted in significantly different bacterial community structures in soils. Firmicutes was prevalent in infested soil, but Chloroflexi and Acidobacteria were prevalent in uninfested soil. <i>Sphingomonas</i>, <i>Streptomyces</i>, and <i>Bradyrhizobium</i> were the dominant bacteria genera, and their abundance were higher in infested soil. By PICRUSt analysis, some metabolism-related functions and signal transduction functions of the rhizosphere bacterial community in the <i>M. incognita</i> infection-tobacco plants had a higher relative abundance than those uninfected. As a result, rhizosphere soils from tobacco plants infected with <i>M. incognita</i> showed considerable bacterial community structure and function alterations.
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Kim, Eun-Tae, Sang-Jin Lee, Tae-Yong Kim, Hyo-Gun Lee, Rahman M. Atikur, Bon-Hee Gu, Dong-Hyeon Kim, Beom-Young Park, Jun-Kyu Son, and Myung-Hoo Kim. "Dynamic Changes in Fecal Microbial Communities of Neonatal Dairy Calves by Aging and Diarrhea." Animals 11, no. 4 (April 13, 2021): 1113. http://dx.doi.org/10.3390/ani11041113.
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Microbiota plays a critical role in the overall growth performance and health status of dairy cows, especially during their early life. Several studies have reported that fecal microbiome of neonatal calves is shifted by various factors such as diarrhea, antibiotic treatment, or environmental changes. Despite the importance of gut microbiome, a lack of knowledge regarding the composition and functions of microbiota impedes the development of new strategies for improving growth performance and disease resistance during the neonatal calf period. In this study, we utilized next-generation sequencing to monitor the time-dependent dynamics of the gut microbiota of dairy calves before weaning (1–8 weeks of age) and further investigated the microbiome changes caused by diarrhea. Metagenomic analysis revealed that continuous changes, including increasing gut microbiome diversity, occurred from 1 to 5 weeks of age. However, the composition and diversity of the fecal microbiome did not change after 6 weeks of age. The most prominent changes in the fecal microbiome composition caused by aging at family level were a decreased abundance of Bacteroidaceae and Enterobacteriaceae and an increased abundance of Prevotellaceae. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis indicated that the abundance of microbial genes associated with various metabolic pathways changed with aging. All calves with diarrhea symptoms showed drastic microbiome changes and about a week later returned to the microbiome of pre-diarrheal stage regardless of age. At phylum level, abundance of Bacteroidetes was decreased (p = 0.09) and that of Proteobacteria increased (p = 0.07) during diarrhea. PICRUSt analysis indicated that microbial metabolism-related genes, such as starch and sucrose metabolism, sphingolipid metabolism, alanine aspartate, and glutamate metabolism were significantly altered in diarrheal calves. Together, these results highlight the important implications of gut microbiota in gut metabolism and health status of neonatal dairy calves.
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Cornejo-Pareja, Isabel, Patricia Ruiz-Limón, Ana M. Gómez-Pérez, María Molina-Vega, Isabel Moreno-Indias, and Francisco J. Tinahones. "Differential Microbial Pattern Description in Subjects with Autoimmune-Based Thyroid Diseases: A Pilot Study." Journal of Personalized Medicine 10, no. 4 (October 26, 2020): 192. http://dx.doi.org/10.3390/jpm10040192.
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The interaction between genetic susceptibility, epigenetic, endogenous, and environmental factors play a key role in the initiation and progression of autoimmune thyroid diseases (AITDs). Studies have shown that gut microbiota alterations take part in the development of autoimmune diseases. We have investigated the possible relationship between gut microbiota composition and the most frequent AITDs. A total of nine Hashimoto’s thyroiditis (HT), nine Graves–Basedow’s disease (GD), and 11 otherwise healthy donors (HDs) were evaluated. 16S rRNA pyrosequencing and bioinformatics analysis by Quantitative Insights into Microbial Ecology and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) were used to analyze the gut microbiota. Beta diversity analysis showed that gut microbiota from our groups was different. We observed an increase in bacterial richness in HT and a lower evenness in GD in comparison to the HDs. GD showed a significant increase of Fusobacteriaceae, Fusobacterium and Sutterella compared to HDs and the core microbiome features showed that Prevotellaceae and Prevotella characterized this group. Victivallaceae was increased in HT and was part of their core microbiome. Streptococcaceae, Streptococcus and Rikenellaceae were greater in HT compared to GD. Core microbiome features of HT were represented by Streptococcus, Alistipes, Anaerostipes, Dorea and Haemophilus. Faecalibacterium decreased in both AITDs compared to HDs. PICRUSt analysis demonstrated enrichment in the xenobiotics degradation, metabolism, and the metabolism of cofactors and vitamins in GD patients compared to HDs. Moreover, correlation studies showed that some bacteria were widely correlated with autoimmunity parameters. A prediction model evaluated a possible relationship between predominant concrete bacteria such as an unclassified genus of Ruminococcaceae, Sutterella and Faecalibacterium in AITDs. AITD patients present altered gut microbiota compared to HDs. These alterations could be related to the immune system development in AITD patients and the loss of tolerance to self-antigens.
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Wu, Linkun, Bo Yang, Manlin Li, Jun Chen, Zhigang Xiao, Hongmiao Wu, Qingyu Tong, Xiaomian Luo, and Wenxiong Lin. "Modification of Rhizosphere Bacterial Community Structure and Functional Potentials to Control Pseudostellaria heterophylla Replant Disease." Plant Disease 104, no. 1 (January 2020): 25–34. http://dx.doi.org/10.1094/pdis-04-19-0833-re.
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Replant disease caused by negative plant-soil feedback commonly occurs in a Pseudostellaria heterophylla monoculture regime. Here, barcoded pyrosequencing of 16S ribosomal DNA amplicons combined with phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis was applied to study the shifts in soil bacterial community structure and functional potentials in the rhizosphere of P. heterophylla under consecutive monoculture and different soil amendments (i.e., bio-organic fertilizer application [MF] and paddy-upland rotation [PR]). The results showed that the yield of tuberous roots decreased under P. heterophylla consecutive monoculture and then increased after MF and PR treatments, which was consistent with the changes in soil bacterial diversity. Both principal coordinate analysis and the unweighted pair-group method with arithmetic means cluster analysis showed the distinct difference in bacterial community structure between the consecutively monocultured soil (relatively unhealthy soil) and other relatively healthy soils (i.e., newly planted soil, MF, and PR). Furthermore, taxonomic analysis showed that consecutive monoculture of P. heterophylla significantly decreased the relative abundances of the families Burkholderiaceae and Acidobacteriaceae (subgroup 1), whereas it increased the population density of families Xanthomonadaceae, Phyllobacteriaceae, Sphingobacteriaceae, and Alcaligenaceae, and Fusarium oxysporum. In contrast, the MF and PR treatments recovered the soil microbiome and decreased F. oxysporum abundance through the different ways; for example, the introduction of beneficial microorganisms (in MF) or the switching between anaerobic and aerobic conditions (in PR). In addition, PICRUSt analysis revealed the higher abundances of membrane transport, cell motility, and DNA repair in the consecutively monocultured soil, which might contribute to the root colonization and survival for certain bacterial pathogens under monoculture. These findings highlight the close association between replant disease of P. heterophylla and the variations in structure and potential functions of rhizosphere bacterial community.
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Chang, Fan, Fengan Jia, Rui Lv, Lisha Zhen, Yan Li, and Yan Wang. "Changes in structure and function of bacterial and fungal communities in open composting of Chinese herb residues." Canadian Journal of Microbiology 66, no. 3 (March 2020): 194–205. http://dx.doi.org/10.1139/cjm-2019-0347.
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In this study, dynamic changes in bacterial and fungal communities, metabolic characteristics, and trophic modes in Chinese herb residues open composting for 30 days were analyzed by using high-throughput sequencing, PICRUSt, and FUNGuild, respectively. Bacillaceae and Basidiomycota predominated at the early composting stage, while Proteobacteria and Ascomycota became the dominant phyla during the active phase. Aerobic composting had a significant effect on bacterial metabolic characteristics and fungal trophic modes over the composting time. The function of the bacterial communities changed from environmental information processing to metabolism. Fungal communities changed as well, with the pathogenic fungi decreasing and wood saprotrophs increasing. These results indicated that open composting of Chinese herb residues not only influenced microbial community structure but also changed metabolic characteristics and trophic modes, which became the internal dynamics of composting.
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Wang, Ying, Jianqing Zhu, Jie Fang, Li Shen, Shuojia Ma, Zimiao Zhao, Weidong Yu, and Weibin Jiang. "Diversity, Composition and Functional Inference of Gut Microbiota in Indian Cabbage white Pieris canidia (Lepidoptera: Pieridae)." Life 10, no. 11 (October 25, 2020): 254. http://dx.doi.org/10.3390/life10110254.
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We characterized the gut microbial composition and relative abundance of gut bacteria in the larvae and adults of Pieris canidia by 16S rRNA gene sequencing. The gut microbiota structure was similar across the life stages and sexes. The comparative functional analysis on P. canidia bacterial communities with PICRUSt showed the enrichment of several pathways including those for energy metabolism, immune system, digestive system, xenobiotics biodegradation, transport, cell growth and death. The parameters often used as a proxy of insect fitness (development time, pupation rate, emergence rate, adult survival rate and weight of 5th instars larvae) showed a significant difference between treatment group and untreated group and point to potential fitness advantages with the gut microbiomes in P. canidia. These data provide an overall view of the bacterial community across the life stages and sexes in P. canidia.
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Wang, Hui, Zhaojun Chen, Mei Wang, Mingxiu Long, Tingyuan Ren, Chao Chen, Xiaotong Dai, Sheng Yang, and Shuming Tan. "The Effect of Polyphenol Extract from Rosa Roxburghii Fruit on Plasma Metabolome and Gut Microbiota in Type 2 Diabetic Mice." Foods 11, no. 12 (June 14, 2022): 1747. http://dx.doi.org/10.3390/foods11121747.
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Rosa roxburghii fruit is an underutilized functional food abundant in polyphenols. Polyphenols have been proved to have antidiabetic effects. This study investigates the effects of Rosa roxburghii fruit polyphenols extract (RPE) on plasma metabolites and gut microbiota composition in streptozotocin (STZ)- and high-fat diet- induced type 2 diabetes using metabolomics and 16S rRNA gene sequencing. The induced diabetic mice were fed with 400 mg/kg body weight RPE for 8 weeks. RPE demonstrated hypoglycemic, hypolipidemic, and anti-inflammatory effects. Colonic oxidative stress biomarkers were also lowered by RPE. Besides, RPE decreased plasma ceramides and tyrosine levels and increased carnitine and phosphatidylinositols levels, indicating improved insulin resistance, lipid metabolism, and immune response. Furthermore, RPE decreased abundances of Lachnospiraceae and Rikenellaceae and increased abundances of Erysipelotrichaceae and Faecalibaculum. Metabolic function prediction of the gut microbiota by PICRUSt demonstrated that RPE downregulated the phosphotransferase system. Taken together, these findings demonstrated that RPE has the potential to prevent type 2 diabetes by regulating the plasma metabolites and gut microbes.
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García-Márquez, Jorge, Isabel M. Cerezo, Félix L. Figueroa, Roberto Teófilo Abdala-Díaz, and Salvador Arijo. "First Evaluation of Associated Gut Microbiota in Wild Thick-Lipped Grey Mullets (Chelon labrosus, Risso 1827)." Fishes 7, no. 4 (August 19, 2022): 209. http://dx.doi.org/10.3390/fishes7040209.
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This study aimed to characterize the intestinal microbiota of wild thick-lipped grey mullets (Chelon labrosus) and explore its potential functionality on the host. Intestinal contents of anterior and posterior sections from wild fish were collected and DNA was extracted. Subsequently, the V3–V4 regions of 16S rRNA were sequenced using the Illumina technology and results were analyzed by bioinformatics pipeline. The functional profile of the microbial community was analyzed using PICRUSt software. Shannon and Simpson diversity indices were significantly higher in the posterior section of wild specimens. The overall taxonomic composition suggests a certain homogeneity in the anterior section of the intestine and heterogeneity in the posterior section. Due to this, no statistical differences were detected at any level among both intestinal sections. Predicted functions of intestinal microbiota showed the most abundant were those related to amino acid metabolism, carbohydrate metabolism, energy metabolism, membrane transport, and cell replication and repair. Furthermore, the analysis revealed microbial functional genes related to the elimination of environmental toxins.
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Chen, Yan, Wei Tian, Yang Shao, Ying-Jun Li, Li-An Lin, Ying-Jun Zhang, Hui Han, and Zhao-Jin Chen. "Miscanthus cultivation shapes rhizosphere microbial community structure and function as assessed by Illumina MiSeq sequencing combined with PICRUSt and FUNGUIld analyses." Archives of Microbiology 202, no. 5 (February 17, 2020): 1157–71. http://dx.doi.org/10.1007/s00203-020-01830-1.
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Liang, Xiubin, Mohamad Bouhamdan, Xia Hou, Kezhong Zhang, Jun Song, Ke Hao, Jian-Ping Jin, Zhongyang Zhang, and Jie Xu. "Intestinal Dysbiosis in Young Cystic Fibrosis Rabbits." Journal of Personalized Medicine 11, no. 2 (February 16, 2021): 132. http://dx.doi.org/10.3390/jpm11020132.
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Individuals with cystic fibrosis (CF) often experience gastrointestinal (GI) abnormalities. In recent years, the intestinal microbiome has been postulated as a contributor to the development of CF-associated GI complications, hence representing a potential therapeutic target for treatment. We recently developed a rabbit model of CF, which is shown to manifest many human patient-like pathological changes, including intestinal obstruction. Here, we investigated the feces microbiome in young CF rabbits in the absence of antibiotics treatment. Stool samples were collected from seven- to nine-week-old CF rabbits (n = 7) and age-matched wild-type (WT) rabbits (n = 6). Microbiomes were investigated by iTag sequencing of 16S rRNA genes, and functional profiles were predicted using PICRUSt. Consistent with reports of those in pediatric CF patients, the fecal microbiomes of CF rabbits are of lower richness and diversity than that of WT rabbits, with a marked taxonomic and inferred functional dysbiosis. Our work identified a new CF animal model with the manifestation of intestinal dysbiosis phenotype. This model system may facilitate the research and development of novel treatments for CF-associated gastrointestinal diseases.
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Raghunathan, N., V. Joshi, R. Patel, D. Mekala, P. Pal, and R. Banerjee. "P924 A unique gut microbiome signature can help differentiate Crohn`s Disease and isolated Terminal Ileitis." Journal of Crohn's and Colitis 17, Supplement_1 (January 30, 2023): i1033—i1035. http://dx.doi.org/10.1093/ecco-jcc/jjac190.1054.
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Abstract Background With increasing number of ileal intubations, isolated terminal ileal ulcers(TI) are often detected during colonoscopies. The etiology of these lesions have not been well-defined and differentiating TI from early Crohn’s Disease (CD) is a commonly encountered diagnostic challenge. CD is associated with significant dysbiosis; however, the gut microbiome of TI is poorly studied. We aimed to compare the gut microbial profile between CD and isolated non-specific TI. Methods Fecal samples were collected from treatment naïve patients (26 CD;13 TI) and healthy volunteers (29) without the use of antibiotics, probiotics, and prebiotics for at least 6 weeks. CD was confirmed by endoscopic and histological examination. TI was diagnosed based on isolated terminal ileal erosions/ulcers, normal small bowel endoscopy, non-specific inflammation with no granulomas/ cryptitis/crypt abscess on biopsy, and no history of NSAIDs. Fecal DNA was isolated and sequenced(16S-V4). Taxonomical classification was performed by Amplicon Sequence Variant approach and analysed by STAMP (Statistical Analysis of Metagenomic Profiles) using Welch`s T-Test. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was used for predictive metagenomics. Significant metabolic pathways were corrected by Storey FDR (q<0.05). Fecal Calprotectin (FCal) was measured using QuantOnCal rapid test. Results Microbiome data analysis revealed a progressive decline in α-diversity(p=0.002) in CD and different β-diversity (Bray-Curtis dissimilarity p=0.001) compared to TI and healthy(Fig1). Overall Firmicutes were lower(p=9.81e-4) while Desulfobacterota were higher(p=8.65e-3) in CD than TI(Fig2A). Faecalibacterium prausnitzii (p=0.04) and Roseburia inulinivorans (p=0.03) were markedly reduced while Parabacteroides distasonis (p=9.91e-3) and Bilophila wadsworthia (p=7.36e-3) were elevated in CD (Fig3). A microbial signature covering 8 non-overlapping taxa was deduced to distinguish CD and TI (3 taxa reduced, 5 elevated in CD compared to TI) (Fig2B). PICRUSt analysis indicated 18 significant metabolic pathways differentiating CD and TI. Bacterial stress alarmone PPGPP-MET was significantly higher in CD (p=2.04e-3) (Fig4). FCal was significantly higher in CD with mean value (±SD) as 549.12±390.4 and 167.15±191.8µg/g in TI (p=0.002). Conclusion A distinct gut microbiome profile was observed in TI compared to CD. Exploitation of these differences can potentiate differential diagnosis of CD and TI. Further research on the spectrum of dysbiosis is warranted. This may help in differentiating patients with early-CD who require active therapy from those with non-specific TI ulcers that resolve over time.
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Ahmad, Tawseef, Gaganjot Gupta, Anshula Sharma, Baljinder Kaur, Mohamed A. El-Sheikh, and Mohammed Nasser Alyemeni. "Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake." PLOS ONE 16, no. 3 (March 25, 2021): e0248116. http://dx.doi.org/10.1371/journal.pone.0248116.
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Freshwater lakes present an ecological border between humans and a variety of host organisms. The present study was designed to evaluate the microbiota composition and distribution in Dal Lake at Srinagar, India. The non-chimeric sequence reads were classified taxonomically into 49 phyla, 114 classes, 185 orders, 244 families and 384 genera. Proteobacteria was found to be the most abundant bacterial phylum in all the four samples. The highest number of observed species was found to be 3097 in sample taken from least populated area during summer (LPS) whereas the summer sample from highly populated area (HPS) was found most diverse among all as indicated by taxonomic diversity analysis. The QIIME output files were used for PICRUSt analysis to assign functional attributes. The samples exhibited a significant difference in their microbial community composition and structure. Comparative analysis of functional pathways indicated that the anthropogenic activities in populated areas and higher summer temperature, both decrease functional potential of the Lake microbiota. This is probably the first study to demonstrate the comparative taxonomic diversity and functional composition of an urban freshwater lake amid its highly populated and least populated areas during two extreme seasons (winter and summer).
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Shen, Hailiang, Linhua Huang, Huating Dou, Yali Yang, and Houjiu Wu. "Effect of Trilobatin from Lithocarpus polystachyus Rehd on Gut Microbiota of Obese Rats Induced by a High-Fat Diet." Nutrients 13, no. 3 (March 10, 2021): 891. http://dx.doi.org/10.3390/nu13030891.
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Trilobatin was identified as the primary bioactive component in the Lithocarpus polystachyus Rehd (LPR) leaves. This study explored the antiobesity effect of trilobatin from LPR leaves and its influence on gut microbiota in obese rats. Results showed that trilobatin could significantly reduce body and liver weight gain induced by a high-fat diet, and the accumulation of perirenal fat, epididymal fat, and brown fat of SD (Male Sprague–Dawley) obese rats in a dose-independent manner. Short-chain fatty acids (SCFAs) concentrations increased, especially the concentration of butyrate. Trilobatin supplementation could significantly increase the relative abundance of Lactobacillus, Prevotella, CF231, Bacteroides, and Oscillospira, and decrease greatly the abundance of Blautia, Allobaculum, Phascolarctobacterium, and Coprococcus, resulting in an increase of the ratio of Bacteroidetes to Firmicutes (except the genera of Lactobacillus and Oscillospira). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway predicted by the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) indicated the different relative metabolic pathways after trilobatin supplementation. This study may reveal the contribution of gut microbiota to the antiobesity effect of trilobatin from LPR leaves and predict the potential regulatory mechanism for obesity induced by a high-fat diet.
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Jauvain, Marine, Sarah Courtois, Philippe Lehours, and Emilie Bessède. "Metformin Modifies the Gut Microbiota of Mice Infected with Helicobacter pylori." Pharmaceuticals 14, no. 4 (April 3, 2021): 329. http://dx.doi.org/10.3390/ph14040329.
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Metformin is widely prescribed to treat type 2 diabetes. Diabetes patients treated with metformin have a decreased risk of cancers, including gastric cancer. Among the factors influencing digestive carcinogenesis, gut microbiota interactions have been intensively studied. Metformin exhibits direct antimicrobial activity toward Helicobacterpylori, which plays a crucial role in gastric carcinogenesis. Mice were infected with H. pylori and treated for 12 days with either metformin or phosphate-buffered saline (PBS) as a control. At the end of the treatment period, the mice were euthanized and cecal and intestinal contents and stool were collected. The gut microbiota of the three different digestive sites (stool, cecal, and intestinal contents) were characterized through 16S RNA gene sequencing. In mice infected with H. pylori, metformin significantly decreased alpha diversity indices and led to significant variation in the relative abundance of some bacterial taxa including Clostridium and Lactobacillus, which were directly inhibited by metformin in vitro. PICRUSt analysis suggested that metformin modifies functional pathway expression, including a decrease in nitrate reducing bacteria in the intestine. Metformin significantly changed the composition and predicted function of the gut microbiota of mice infected with H. pylori; these modifications could be implicated in digestive cancer prevention.
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Xin, Yu, Linhui Ji, Zihao Wang, Kun Li, Xiaoya Xu, and Dufa Guo. "Functional Diversity and CO2 Emission Characteristics of Soil Bacteria during the Succession of Halophyte Vegetation in the Yellow River Delta." International Journal of Environmental Research and Public Health 19, no. 19 (October 9, 2022): 12919. http://dx.doi.org/10.3390/ijerph191912919.
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Carbon dioxide (CO2) is the most important greenhouse gas in the atmosphere, which is mainly derived from microbial respiration in soil. Soil bacteria are an important part of the soil ecosystem and play an important role in the process of plant growth, mineralization, and decomposition of organic matter. In this paper, we discuss a laboratory incubation experiment that we conducted to investigate the CO2 emissions and the underlying bacterial communities under the natural succession of halophyte vegetation in the Yellow River Delta by using high-throughput sequencing technology and PICRUSt functional prediction. The results showed that the bacterial abundance and diversity increased significantly along with the succession of halophyte vegetation. Metabolic function is the dominant function of soil bacteria in the study area. With the succession of halophyte vegetation, the rate of CO2 emissions gradually increased, and were significantly higher in soil covered with vegetation than that of the bare land without vegetation coverage. These results helped to better understand the relationships of soil bacterial communities under the background of halophyte vegetation succession, which can help to make efficient strategies to mitigate CO2 emissions and enhance carbon sequestration.
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Meng, Lixue, Changxiu Xia, Zhixiong Jin, and Hongyu Zhang. "Investigation of Gut Bacterial Communities of Asian Citrus Psyllid (Diaphorina citri) Reared on Different Host Plants." Insects 13, no. 8 (August 2, 2022): 694. http://dx.doi.org/10.3390/insects13080694.
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Diaphorina citri Kuwayama (Hemiptera: Liviidae) can cause severe damage to citrus plants, as it transmits Candidatus Liberibacter spp., a causative agent of Huanglongbing disease. Symbiotic bacteria play vital roles in the ecology and biology of herbivore hosts, thereby affecting host growth and adaptation. In our research, the effects of Rutaceous plants (i.e., Citrus reticulata cv. Shatangju, Citrus poonensis cv. Ponkan, Murraya paniculata (orange jasmine), Citrus limon (lemon), and Citrus sinensis (navel orange)) on the gut microbiota (GM) and microbial diversity of D. citri adults were investigated by 16S rRNA high-throughput sequencing. It was found that Proteobacteria dominated the GM communities. The gut microbe diversity was the highest in the ponkan-feeding population, and the lowest in the Shatangju-feeding population. The NMDS analysis revealed that there were obvious differences in the GM communities among the different hosts. PICRUSt function prediction indicated significant differences in host function, and those pathways were crucial for maintaining population reproduction, growth, development, and adaptation to environmental stress in D. citri. Our study sheds new light on the interactions between symbionts, herbivores, and host plants and expands our knowledge on host adaptation related to GM in D. citri.
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Chukwuma, Ogechukwu Bose, Mohd Rafatullah, Husnul Azan Tajarudin, and Norli Ismail. "Bacterial Diversity and Community Structure of a Municipal Solid Waste Landfill: A Source of Lignocellulolytic Potential." Life 11, no. 6 (May 28, 2021): 493. http://dx.doi.org/10.3390/life11060493.
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Omics have given rise to research on sparsely studied microbial communities such as the landfill, lignocellulolytic microorganisms and enzymes. The bacterial diversity of Municipal Solid Waste sediments was determined using the illumina MiSeq system after DNA extraction and Polymerase chain reactions. Data analysis was used to determine the community’s richness, diversity, and correlation with environmental factors. Physicochemical studies revealed sites with mesophilic and thermophilic temperature ranges and a mixture of acidic and alkaline pH values. Temperature and moisture content showed the highest correlation with the bacteria community. The bacterial analysis of the community DNA revealed 357,030 effective sequences and 1891 operational taxonomic units (OTUs) assigned. Forty phyla were found, with the dominant phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidota, while Aerococcus, Stenotrophomonas, and Sporosarcina were the dominant species. PICRUSt provided insight on community’s metabolic function, which was narrowed down to search for lignocellulolytic enzymes’ function. Cellulase, xylanase, esterase, and peroxidase were gene functions inferred from the data. This article reports on the first phylogenetic analysis of the Pulau Burung landfill bacterial community. These results will help to improve the understanding of organisms dominant in the landfill and the corresponding enzymes that contribute to lignocellulose breakdown.
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Zhang, Qingchao, Qinglin Wang, Yifan Zhai, Hao Zheng, and Xiaofei Wang. "Impacts of Imidacloprid and Flupyradifurone Insecticides on the Gut Microbiota of Bombus terrestris." Agriculture 12, no. 3 (March 10, 2022): 389. http://dx.doi.org/10.3390/agriculture12030389.
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Bumblebees are important pollinators for crops and wild flowering plants. Various pesticides have threatened the abundance and diversity of bumblebees. In addition to direct sublethal effects, pesticides may alter the gut microbial communities of bees. Imidacloprid and flupyradifurone insecticides both bind to the nicotinic acetylcholine receptor. However, the latter was assumed to be harmless for honeybees and can even be applied to flowering crops. In this study, we assessed the impacts of these two pesticides on queenless microcolonies and the gut microbiota of Bombus terrestris. We found that 10 μg/L imidacloprid significantly impeded syrup consumption, and postponed the egg-laying period, larvae, and pupae development. It decreased the relative abundance of the bumblebee-specific symbionts, Apibacter and Lactobacillus Firm-5. On the contrary, 10 μg/L flupyradifurone did not reduce syrup consumption, block larvae and pupae development in bumblebees. Although no significant phenotypes were observed, PICRUST revealed that flupyradifurone suppressed pathways, involving carbohydrate metabolism, nucleotide metabolism, translation, and membrane transport. Our findings suggest the appropriate use of this new pesticide may be considered safe for bumblebees, but the underlying mechanism warrants further investigation.
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Li, Tiange, Yue Zhang, Jiajia Song, Lijun Chen, Min Du, and Xueying Mao. "Yogurt Enriched with Inulin Ameliorated Reproductive Functions and Regulated Gut Microbiota in Dehydroepiandrosterone-Induced Polycystic Ovary Syndrome Mice." Nutrients 14, no. 2 (January 10, 2022): 279. http://dx.doi.org/10.3390/nu14020279.
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The effects of synbiotic yogurt supplemented with inulin on the pathological manifestations and gut microbiota–bile acid axis were investigated using a dehydroepiandrosterone (DHEA)-induced polycystic ovary syndrome (PCOS) mice model. Female C57BL/6J mice were injected subcutaneously with DHEA at a dose of 6 mg/100 g BW for 20 days to establish a PCOS mouse model. Then, the PCOS mice were treated with yogurt containing inulin (6% w/w) at 15 mL/kg BW for 24 days. Results showed that supplementation of synbiotic yogurt enriched with inulin to PCOS mice decreased the body weight gain, improved estrus cycles and ovary morphology, and reduced the levels of luteinizing hormone while increasing the levels of follicle-stimulating hormone and interleukin-22 in serum. At the genus level, synbiotic yogurt increased the relative abundance of Lactobacillus, Bifidobacterium, and Akkermansia. PICRUSt analysis indicated that KEGG pathways including bile acid biosynthesis were changed after inulin-enriched synbiotic yogurt supplementation. Synbiotic yogurt enriched with inulin also modulated the bile acid profiles. In conclusion, inulin-enriched synbiotic yogurt alleviated reproductive dysfunction and modulated gut microbiota and bile acid profiles in PCOS mice.
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Szafranek-Nakonieczna, Anna, Anna Pytlak, Jarosław Grządziel, Adam Kubaczyński, Artur Banach, Andrzej Górski, Weronika Goraj, Agnieszka Kuźniar, Anna Gałązka, and Zofia Stępniewska. "Changes in the Substrate Source Reveal Novel Interactions in the Sediment-Derived Methanogenic Microbial Community." International Journal of Molecular Sciences 20, no. 18 (September 8, 2019): 4415. http://dx.doi.org/10.3390/ijms20184415.
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Methanogenesis occurs in many natural environments and is used in biotechnology for biogas production. The efficiency of methane production depends on the microbiome structure that determines interspecies electron transfer. In this research, the microbial community retrieved from mining subsidence reservoir sediment was used to establish enrichment cultures on media containing different carbon sources (tryptone, yeast extract, acetate, CO2/H2). The microbiome composition and methane production rate of the cultures were screened as a function of the substrate and transition stage. The relationships between the microorganisms involved in methane formation were the major focus of this study. Methanogenic consortia were identified by next generation sequencing (NGS) and functional genes connected with organic matter transformation were predicted using the PICRUSt approach and annotated in the KEGG. The methane production rate (exceeding 12.8 mg CH4 L−1 d−1) was highest in the culture grown with tryptone, yeast extract, and CO2/H2. The analysis of communities that developed on various carbon sources casts new light on the ecophysiology of the recently described bacterial phylum Caldiserica and methanogenic Archaea representing the genera Methanomassiliicoccus and Methanothrix. Furthermore, it is hypothesized that representatives of Caldiserica may support hydrogenotrophic methanogenesis.
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King, Madeline, Padmanabhan Ramnarayan, Sarah E. Seaton, and Christina Pagel. "Modelling the allocation of paediatric intensive care retrieval teams in England and Wales." Archives of Disease in Childhood 104, no. 10 (February 11, 2019): 962–66. http://dx.doi.org/10.1136/archdischild-2018-316056.
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BackgroundFollowing centralisation of UK paediatric intensive care units in 1997, specialist paediatric intensive care retrieval teams (PICRTs) were established to transport critically ill children from district general hospitals (DGHs). The current location and catchment area of PICRTs covering England and Wales are based on historical referral patterns. National quality standards specify that PICRTs should reach the patient bedside within 3 hours of accepting a referral.ObjectiveTo determine what proportion of demand for PICRT services in England and Wales can be reached within 3 hours and to explore the potential coverage impact of more stringent ‘time to bedside’ standards.MethodsWe used mathematical location–allocation methods to: (1) determine the optimal allocation of DGHs to current PICRT locations to minimise road journey time and calculated the proportion of demand reachable within 3 hours, 2 hours, 90 min, 75 min and 1 hour and (2) explore the impact of changing the number and location of PICRTs on demand coverage for the different time thresholds.ResultsFor current (and optimal) location of 11 PICRTs, 98% (98%) of demand is reachable within 3 hours; 86% (91%) within 2 hours; 59% (69%) within 90 min; 33% (39%) within 75 min; and 20% (20%) within 1 hour. Five hospitals were not reachable within 3 hours. For the 3-hour standard, eight optimally located PICRT locations had similar coverage as the current 11 locations.ConclusionsIf new evidence supports reduction in the time to bedside standard, many more hospitals will not be adequately covered. Location–allocation optimisation is a powerful technique for supporting evidence-based service configuration.
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Huyben, David, Simona Rimoldi, Chiara Ceccotti, Daniel Montero, Monica Betancor, Federica Iannini, and Genciana Terova. "Effect of dietary oil from Camelina sativa on the growth performance, fillet fatty acid profile and gut microbiome of gilthead Sea bream (Sparus aurata)." PeerJ 8 (December 9, 2020): e10430. http://dx.doi.org/10.7717/peerj.10430.
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Background In the last two decades, research has focused on testing cheaper and sustainable alternatives to fish oil (FO), such as vegetable oils (VO), in aquafeeds. However, FO cannot be entirely replaced by VOs due to their lack of omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA), particularly eicosapentaenoic (EPA; 20:5n-3) and docosahexaenoic (DHA; 22:6n-3) acids. The oilseed plant, Camelina sativa, may have a higher potential to replace FO since it can contains up to 40% of the omega-3 precursors α-linolenic acid (ALA; 18:3n-3) and linoleic acid (LA; 18:2n-6). Methods A 90-day feeding trial was conducted with 600 gilthead sea bream (Sparus aurata) of 32.92 ± 0.31 g mean initial weight fed three diets that replaced 20%, 40% and 60% of FO with CO and a control diet of FO. Fish were distributed into triplicate tanks per diet and with 50 fish each in a flow-through open marine system. Growth performance and fatty acid profiles of the fillet were analysed. The Illumina MiSeq platform for sequencing of 16S rRNA gene and Mothur pipeline were used to identify bacteria in the faeces, gut mucosa and diets in addition to metagenomic analysis by PICRUSt. Results and Conclusions The feed conversion rate and specific growth rate were not affected by diet, although final weight was significantly lower for fish fed the 60% CO diet. Reduced final weight was attributed to lower levels of EPA and DHA in the CO ingredient. The lipid profile of fillets were similar between the dietary groups in regards to total saturated, monounsaturated, PUFA (n-3 and n-6), and the ratio of n-3/n-6. Levels of EPA and DHA in the fillet reflected the progressive replacement of FO by CO in the diet and the EPA was significantly lower in fish fed the 60% CO diet, while ALA was increased. Alpha and beta-diversities of gut bacteria in both the faeces and mucosa were not affected by any dietary treatment, although a few indicator bacteria, such as Corynebacterium and Rhodospirillales, were associated with the 60% CO diet. However, lower abundance of lactic acid bacteria, specifically Lactobacillus, in the gut of fish fed the 60% CO diet may indicate a potential negative effect on gut microbiota. PICRUSt analysis revealed similar predictive functions of bacteria in the faeces and mucosa, although a higher abundance of Corynebacterium in the mucosa of fish fed 60% CO diet increased the KEGG pathway of fatty acid synthesis and may act to compensate for the lack of fatty acids in the diet. In summary, this study demonstrated that up to 40% of FO can be replaced with CO without negative effects on growth performance, fillet composition and gut microbiota of gilthead sea bream.
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Solovyev, Mikhail M., Elena N. Kashinskaya, Nickolai A. Bochkarev, Karl B. Andree, and Evgeniy Simonov. "The effect of diet on the structure of gut bacterial community of sympatric pair of whitefishes (Coregonus lavaretus): one story more." PeerJ 7 (December 3, 2019): e8005. http://dx.doi.org/10.7717/peerj.8005.
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In the Coregonus lavaretus complex may be found lacustrine sympatric pairs, which serves as an intriguing model for studying different aspects of fish evolutionary biology. One such sympatric whitefish pair inhabits Teletskoye Lake (West Siberia, Russia) and includes a “large” form (Coregonus lavaretus pidschian (Gmelin, 1789)) and a “small” form (C. l. pravdinellus (Dulkeit, 1949)). C. l. pravdinellus has a narrow trophic specialization and feeds on zooplankton, whereas the diet of C. l. pidschian is based on benthic prey. In the present study we aimed to address the question of how the gut microbial community reflects the divergence in diet of a sympatric pair of whitefish. Studied samples included the mucosa and content were collected for cardiac and pyloric stomach, anterior, middle, and posterior intestine, but only mucosa was collected for the pyloric caeca. In addition, water, sediment, macrophyte (environmental microbiota) and invertebrate (microbiota of prey) samples were collected in the same location. The V3–V4 region of the 16S rRNA genes was chosen for microbiome analysis and the software PICRUSt used to estimate the difference functional roles of the microbiota. The number of OTUs and Chao1 index in mucosa and content of cardiac and pyloric stomach were significantly different between whitefish. Significant differences were observed between whitefish for content from different parts of the intestine in terms of OTU number and Chao1 indices, whereas for mucosa from the same parts of intestine these differences were absent. No significant differences were found for diversity estimates of mucosa and content of different parts of the gut (there were a few exceptions) between whitefish. The form of whitefish and the segment of the digestive system were factors with a significant determinative effect on the structure of the microbiota from gut mucosa and content. The most dominant phyla in mucosa and content of cardiac and pyloric stomach was Proteobacteria (57.0–84.0%) for both whitefish. Throughout the intestine of C. l. pidschian the dominant phyla in mucosa were Proteobacteria (38.8%) and Firmicutes (15.6%), whereas for C. l. pravdinellus–Tenericutes (49.6%) and Proteobacteria (28.1%). For both forms, the phylum Spirochaetes was found in a significant amount (20.0–25.0%) in the mucosa of the posterior intestine. While for the content obtained from anterior, middle and posterior intestines, the dominant bacterial phyla were the same as those described for mucosa from the same parts of the intestine for both whitefish. The bacterial community of the prey and environment was significantly different from bacterial communities found for all parts of the gut mucosa for both whitefish, with the exception of the mucosa of the cardiac stomach. According to PICRUSt the highest level of differences between whitefish at the L3 level were found for the intestinal mucosa (75.3%), whereas the lowest one was registered for stomach content (38.8%).
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Thomas, Pious, and Christopher M. M. Franco. "Intracellular Bacteria in Plants: Elucidation of Abundant and Diverse Cytoplasmic Bacteria in Healthy Plant Cells Using In Vitro Cell and Callus Cultures." Microorganisms 9, no. 2 (January 28, 2021): 269. http://dx.doi.org/10.3390/microorganisms9020269.
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This study was initiated to assess whether the supposedly axenic plant cell cultures harbored any cultivation-recalcitrant endophytic bacteria (CREB). Adopting live-cell imaging with bright-field, fluorescent and confocal microscopy and bacterial 16S-rRNA gene taxonomic profiling, we report the cytoplasmic association of abundant and diverse CREBs in long-term actively maintained callus and cell suspension cultures of different plant species. Preliminary bright-field live-cell imaging on grape cell cultures showed abundant intracellular motile micro-particles resembling bacteria, which proved uncultivable on enriched media. Bacterial probing employing DNA stains, transmission electron microscopy, and Eubacterial FISH indicated abundant and diverse cytoplasmic bacteria. Observations on long-term maintained/freshly established callus stocks of different plant species—grapevine, barley, tobacco, Arabidopsis, and medicinal species—indicated intracellular bacteria as a common phenomenon apparently originating from field shoot tissues.Cultivation-independent 16S rRNA gene V3/V3–V4 amplicon profiling on 40-year-old grape cell/callus tissues revealed a high bacterial diversity (>250 genera), predominantly Proteobacteria, succeeded by Firmicutes, Actinobacteria, Bacteriodetes, Planctomycetes, and 20 other phyla, including several candidate phyla. PICRUSt analysis revealed diverse functional roles for the bacterial microbiome, majorly metabolic pathways. Thus, we unearth the widespread association of cultivation-recalcitrant intracellular bacteria “Cytobacts” inhabiting healthy plant cells, sharing a dynamic mutualistic association with cell hosts.
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Pacífico, Cátia, Renée Maxine Petri, Sara Ricci, Elsayed Mickdam, Stefanie Urimare Wetzels, Viktoria Neubauer, and Qendrim Zebeli. "Unveiling the Bovine Epimural Microbiota Composition and Putative Function." Microorganisms 9, no. 2 (February 9, 2021): 342. http://dx.doi.org/10.3390/microorganisms9020342.
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Numerous studies have used the 16S rRNA gene target in an attempt to characterize the structure and composition of the epimural microbiota in cattle. However, comparisons between studies are challenging, as the results show large variations associated with experimental protocols and bioinformatics methodologies. Here, we present a meta-analysis of the rumen epimural microbiota from 11 publicly available amplicon studies to assess key technical and biological sources of variation between experiments. Using the QIIME2 pipeline, 332 rumen epithelial microbiota samples were analyzed to investigate community structure, composition, and functional potential. Despite having a significant impact on microbial abundance, country of origin, farm, hypervariable region, primer set, animal variability, and biopsy location did not obscure the identification of a core microbiota. The bacterial genera Campylobacter, Christensenellaceae R-7 group, Defluviitaleaceae UCG-011, Lachnospiraceae UCG-010, Ruminococcaceae NK4A214 group, Ruminococcaceae UCG-010, Ruminococcaceae UCG-014, Succiniclasticum, Desulfobulbus, and Comamonas spp. were found in nearly all epithelium samples (>90%). Predictive analysis (PICRUSt) was used to assess the potential functions of the epithelial microbiota. Regularized canonical correlation analysis identified several pathways associated with the biosynthesis of precursor metabolites in Campylobacter, Comamonas, Desulfobulbus, and Ruminococcaceae NK4A214, highlighting key metabolic functions of these microbes within the epithelium.
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Panteli, Nikolas, Maria Mastoraki, Maria Lazarina, Stavros Chatzifotis, Eleni Mente, Konstantinos Ar Kormas, and Efthimia Antonopoulou. "Configuration of Gut Microbiota Structure and Potential Functionality in Two Teleosts under the Influence of Dietary Insect Meals." Microorganisms 9, no. 4 (March 28, 2021): 699. http://dx.doi.org/10.3390/microorganisms9040699.
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Insect meals are considered promising, eco-friendly, alternative ingredients for aquafeed. Considering the dietary influence on establishment of functioning gut microbiota, the effect of the insect meal diets on the microbial ecology should be addressed. The present study assessed diet- and species-specific shifts in gut resident bacterial communities of juvenile reared Dicentrarchus labrax and Sparus aurata in response to three experimental diets with insect meals from three insects (Hermetia illucens, Tenebrio molitor, Musca domestica), using high-throughput Illumina sequencing of the V3–V4 region of the 16S rRNA gene. The dominant phyla were Firmicutes, Proteobacteria and Actinobacteria in all dietary treatments. Anaerococcus sp., Cutibacterium sp. and Pseudomonas sp. in D. labrax, and Staphylococcus sp., Hafnia sp. and Aeromonas sp. in S. aurata were the most enriched shared species, following insect-meal inclusion. Network analysis of the dietary treatments highlighted diet-induced changes in the microbial community assemblies and revealed unique and shared microbe-to-microbe interactions. PICRUSt-predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were significantly differentiated, including genes associated with metabolic pathways. The present findings strengthen the importance of diet in microbiota configuration and underline that different insects as fish feed ingredients elicit species-specific differential responses of structural and functional dynamics in gut microbial communities.
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Dube, Joel P., Angel Valverde, Joachim M. Steyn, Don A. Cowan, and Jacqueline E. van der Waals. "Differences in Bacterial Diversity, Composition and Function due to Long-Term Agriculture in Soils in the Eastern Free State of South Africa." Diversity 11, no. 4 (April 17, 2019): 61. http://dx.doi.org/10.3390/d11040061.
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Land-use change from natural to managed agricultural ecosystems significantly impacts soil bacterial diversity and function. The Eastern Free State (EFS) is one of the most productive agricultural regions in South Africa. However, no studies aiming to understand the changes in bacterial diversity, composition and function due to land-use change in this area have been conducted. This study investigated, using high-throughput 16S rRNA gene amplicon sequencing, the effects of long-term agriculture on bacterial diversity, composition and putative function in the EFS by comparing microbiomes from lands that have been under agronomic activity for over 50 years to those from uncultivated land. Results indicate that agriculture increased bacterial diversity. Soil chemical analysis showed that land-use shifted soils from being oligotrophic to copiotrophic, which changed bacterial communities from being Actinobacteria dominated to Proteobacteria dominated. Predictive functional analysis using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) suggested that agricultural soil was abundant in genes associated with plant fitness and plant growth promotion, while non-agricultural soil was abundant in genes related to organic matter degradation. Together, these results suggest that edaphic factors induced by long-term agriculture resulted in shifts in bacterial diversity and putative function in the EFS.
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Chen, Xiaojuan, Da He, Lianfeng Zhou, Yankun Cao, and Zhanjing Li. "Influence of hydropower stations on the water microbiota in the downstream of Jinsha River, China." PeerJ 8 (July 16, 2020): e9500. http://dx.doi.org/10.7717/peerj.9500.
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Construction of hydropower stations has been an important approach to meet China’s increasing power demand, but the impact of construction of hydropower stations on river microbiota is not fully understood. To evaluate this, the microbial composition from 18 sampling sites in the downstream of Jinsha River of China, upstream and downstream of two completed and two under-construction hydropower stations, were analyzed using high-throughput 16S rRNA gene sequencing. Three independent samples from each site were analyzed. A total of 18,683 OTUs from 1,350 genera were identified at 97% sequence similarity. Our results showed that the completion of hydropower stations would significantly increase the relative abundances of Acidobacteria, Chlorobi, Chloroflexi, Cyanobacteria, Nitrospirae, and Planctomycetes, especially the relative abundance of Synechococcus dOTUs and thus increase the risk of algal blooms. PCA based on all KEGG pathways and the significantly different KEGG pathways showed the predicted metabolic characteristics of the water microbiota by PICRUSt in the activated hydropower station group were significant difference to the other groups. Results from canonical correspondence analysis showed that water temperature and dissolved oxygen had significant effects on microbiota composition. These results are important for assessing the impact of hydropower stations on river microbiota and their potential environmental risks.
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Lian, Tengxiang, Yinghui Mu, Jian Jin, Qibin Ma, Yanbo Cheng, Zhandong Cai, and Hai Nian. "Impact of intercropping on the coupling between soil microbial community structure, activity, and nutrient-use efficiencies." PeerJ 7 (February 8, 2019): e6412. http://dx.doi.org/10.7717/peerj.6412.
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Sugarcane-soybean intercropping has been widely used to control disease and improve nutrition in the field. However, the response of the soil microbial community diversity and structure to intercropping is not well understood. Since microbial diversity corresponds to soil quality and plant health, a pot experiment was conducted with sugarcane intercropped with soybean. Rhizosphere soil was collected 40 days after sowing, and MiSeq sequencing was utilized to analyze the soil microbial community diversity and composition. Soil columns were used to assess the influence of intercropping on soil microbial activity (soil respiration and carbon-use efficiency: nitrogen-use efficiency ratio). PICRUSt and FUNGuild analysis were conducted to predict microbial functional profiling. Our results showed that intercropping decreased pH by approximately 8.9% and enhanced the soil organic carbon, dissolved organic carbon, and available nitrogen (N) by 5.5%, 13.4%, and 10.0%, respectively. These changes in physicochemical properties corresponded to increased microbial diversity and shifts in soil microbial communities. Microbial community correlated significantly (p < 0.05) with soil respiration rates and nutrient use efficiency. Furthermore, intercropping influenced microbial functions, such as carbon fixation pathways in prokaryotes, citrate cycle (TCA cycle) of bacteria and wood saprotrophs of fungi. These overrepresented functions might accelerate nutrient conversion and control phytopathogens in soil.
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Liu, Qi, Zichen He, Takeshi Naganuma, Ryosuke Nakai, Luz María Rodríguez, Rafael Carreño, and Franco Urbani. "Phylotypic Diversity of Bacteria Associated with Speleothems of a Silicate Cave in a Guiana Shield Tepui." Microorganisms 10, no. 7 (July 11, 2022): 1395. http://dx.doi.org/10.3390/microorganisms10071395.
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The diversity of microorganisms associated with speleological sources has mainly been studied in limestone caves, while studies in silicate caves are still under development. Here, we profiled the microbial diversity of opal speleothems from a silicate cave in Guiana Highlands. Bulk DNAs were extracted from three speleothems of two types, i.e., one soft whitish mushroom-like speleothem and two hard blackish coral-like speleothems. The extracted DNAs were amplified for sequencing the V3–V4 region of the bacterial 16S rRNA gene by MiSeq. A total of 210,309 valid reads were obtained and clustered into 3184 phylotypes or operational taxonomic units (OTUs). The OTUs from the soft whitish speleothem were mostly affiliated with Acidobacteriota, Pseudomonadota (formerly, Proteobacteria), and Chloroflexota, with the OTUs ascribed to Nitrospirota being found specifically in this speleothem. The OTUs from the hard blackish speleothems were similar to each other and were mostly affiliated with Pseudomonadota, Acidobacteriota, and Actinomycetota (formerly, Actinobacteria). These OTU compositions were generally consistent with those reported for limestone and silicate caves. The OTUs were further used to infer metabolic features by using the PICRUSt bioinformatic tool, and membrane transport and amino acid metabolism were noticeably featured. These and other featured metabolisms may influence the pH microenvironment and, consequently, the formation, weathering, and re-deposition of silicate speleothems.
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Bomberg, Malin, Tiina Lamminmäki, and Merja Itävaara. "Microbial communities and their predicted metabolic characteristics in deep fracture groundwaters of the crystalline bedrock at Olkiluoto, Finland." Biogeosciences 13, no. 21 (November 3, 2016): 6031–47. http://dx.doi.org/10.5194/bg-13-6031-2016.
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Abstract. The microbial diversity in oligotrophic isolated crystalline Fennoscandian Shield bedrock fracture groundwaters is high, but the core community has not been identified. Here we characterized the bacterial and archaeal communities in 12 water conductive fractures situated at depths between 296 and 798 m by high throughput amplicon sequencing using the Illumina HiSeq platform. Between 1.7 × 104 and 1.2 × 106 bacterial or archaeal sequence reads per sample were obtained. These sequences revealed that up to 95 and 99 % of the bacterial and archaeal sequences obtained from the 12 samples, respectively, belonged to only a few common species, i.e. the core microbiome. However, the remaining rare microbiome contained over 3- and 6-fold more bacterial and archaeal taxa. The metabolic properties of the microbial communities were predicted using PICRUSt. The approximate estimation showed that the metabolic pathways commonly included fermentation, fatty acid oxidation, glycolysis/gluconeogenesis, oxidative phosphorylation, and methanogenesis/anaerobic methane oxidation, but carbon fixation through the Calvin cycle, reductive TCA cycle, and the Wood–Ljungdahl pathway was also predicted. The rare microbiome is an unlimited source of genomic functionality in all ecosystems. It may consist of remnants of microbial communities prevailing in earlier environmental conditions, but could also be induced again if changes in their living conditions occur.
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García-Legorreta, Arantxa, Luis Alfonso Soriano-Pérez, Aline Mariana Flores-Buendía, Omar Noel Medina-Campos, Lilia G. Noriega, Omar Granados-Portillo, Rafael Nambo-Venegas, et al. "Effect of Dietary Magnesium Content on Intestinal Microbiota of Rats." Nutrients 12, no. 9 (September 22, 2020): 2889. http://dx.doi.org/10.3390/nu12092889.
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Background: Magnesium is a mineral that modulates several physiological processes. However, its relationship with intestinal microbiota has been scarcely studied. Therefore, this study aimed to assess the role of dietary magnesium content to modulate the intestinal microbiota of Wistar male rats. Methods: Rats were randomly assigned one of three diets: a control diet (C-Mg; 1000 mg/kg), a low magnesium content diet (L-Mg; 60 mg/kg), and a high magnesium content diet (H-Mg; 6000 mg/kg), for two weeks. After treatment, fecal samples were collected. Microbiota composition was assessed by sequencing the V3–V4 hypervariable region. Results: The C-Mg and L-Mg groups had more diversity than H-Mg group. CF231, SMB53, Dorea, Lactobacillus and Turibacter were enriched in the L-Mg group. In contrast, the phyla Proteobacteria, Parabacteroides, Butyricimonas, and Victivallis were overrepresented in the H-Mg group. PICRUSt analysis indicated that fecal microbiota of the L-Mg group were encoded with an increased abundance of metabolic pathways involving carbohydrate metabolism and butanoate metabolism. Conclusion: Dietary magnesium supplementation can result in intestinal dysbiosis development in a situation where there is no magnesium deficiency. Conversely, low dietary magnesium consumption is associated with microbiota with a higher capacity to harvest energy from the diet.
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Cangioli, Lisa, Marco Mancini, Ada Baldi, Camilla Fagorzi, Simone Orlandini, Francesca Vaccaro, and Alessio Mengoni. "Effect of Site and Phenological Status on the Potato Bacterial Rhizomicrobiota." Microorganisms 10, no. 9 (August 29, 2022): 1743. http://dx.doi.org/10.3390/microorganisms10091743.
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The potato is the fourth major food crop in the world. Its cultivation can encounter problems, resulting in poor growth and reduced yield. Plant microbiota has shown an ability to increase growth and resistance. However, in the development of effective microbiota manipulation strategies, it is essential to know the effect of environmental variables on microbiota composition and function. Here, we aimed to identify the differential impact of the site of cultivation and plant growth stage on potato rhizosphere microbiota. We performed a 16S rRNA gene amplicon sequencing analysis of rhizospheric soil collected from potato plants grown at four sites in central Italy during two phenological stages. Rhizomicrobiota was mainly composed of members of phyla Acidobacteriota, Actinobacteriota, Chloroflexi, and Proteobacteria and was affected by both the site of cultivation and the plant stages. However, cultivation sites overcome the effect of plant phenological stages. The PiCRUST analysis suggested a high abundance of functions related to the biosynthesis of the siderophore enterobactin. The presence of site-specific taxa and functional profiling of the microbiota could be further exploited in long-term studies to evaluate the possibility of developing biomarkers for traceability of the products and to exploit plant growth-promoting abilities in the native potato microbiota.
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Tallei, Trina Ekawati, Fatimawali, Afriza Yelnetty, Diah Kusumawaty, Yunus Effendi, Moon Nyeo Park, Fahad A. Alhumaydhi, Talha Bin Emran, and Bonglee Kim. "Predictive Microbial Community and Functional Gene Expression Profiles in Pineapple Peel Fermentation Using 16S rRNA Gene Sequences." Fermentation 8, no. 5 (April 24, 2022): 194. http://dx.doi.org/10.3390/fermentation8050194.
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Pineapple peel (PP) is a by-product with the potential to be used as a raw material for functional beverages. Traditional PP fermentation has so far paid little attention to the microbial community and its role in the fermentation process. As a result, the current research looked into the microbial communities and their roles during PP fermentation. A metagenomic approach based on the 16S rRNA sequencing data was used to assess the microbial communities. Subsequent analysis was performed using PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states) to analyze the microbial functions in the fermentation system. The microecology of the fermentation process in three samples was predominated by Firmicutes. Furthermore, the well-known probiotic genera Weissella, Lactobacillus, and Lactococcus were found to be predominating in the gumer, promic, and control samples, respectively. It was obvious that microenvironmental differences have an effect on the microbial composition of PP fermentation. Moreover, functional prediction revealed that carbohydrate metabolism was the most prevalent metabolic pathway during the fermentation process. Additionally, it was discovered that all of the bacteria found in the samples played significant roles in carbohydrate, amino acid, vitamin, and co-factor metabolism, which can be inferred to result in the production of beneficial metabolites.
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Tallei, Trina Ekawati, Fatimawali, Afriza Yelnetty, Diah Kusumawaty, Yunus Effendi, Moon Nyeo Park, Fahad A. Alhumaydhi, Talha Bin Emran, and Bonglee Kim. "Predictive Microbial Community and Functional Gene Expression Profiles in Pineapple Peel Fermentation Using 16S rRNA Gene Sequences." Fermentation 8, no. 5 (April 24, 2022): 194. http://dx.doi.org/10.3390/fermentation8050194.
Full textAbstract:
Pineapple peel (PP) is a by-product with the potential to be used as a raw material for functional beverages. Traditional PP fermentation has so far paid little attention to the microbial community and its role in the fermentation process. As a result, the current research looked into the microbial communities and their roles during PP fermentation. A metagenomic approach based on the 16S rRNA sequencing data was used to assess the microbial communities. Subsequent analysis was performed using PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states) to analyze the microbial functions in the fermentation system. The microecology of the fermentation process in three samples was predominated by Firmicutes. Furthermore, the well-known probiotic genera Weissella, Lactobacillus, and Lactococcus were found to be predominating in the gumer, promic, and control samples, respectively. It was obvious that microenvironmental differences have an effect on the microbial composition of PP fermentation. Moreover, functional prediction revealed that carbohydrate metabolism was the most prevalent metabolic pathway during the fermentation process. Additionally, it was discovered that all of the bacteria found in the samples played significant roles in carbohydrate, amino acid, vitamin, and co-factor metabolism, which can be inferred to result in the production of beneficial metabolites.
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Madany, Abdullah M., Heather K. Hughes, and Paul Ashwood. "Antibiotic Treatment during Pregnancy Alters Offspring Gut Microbiota in a Sex-Dependent Manner." Biomedicines 10, no. 5 (April 30, 2022): 1042. http://dx.doi.org/10.3390/biomedicines10051042.
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This study investigated the effect of antibiotics administered to pregnant dams on offspring gut microbiome composition and metabolic capabilities, and how these changes in the microbiota may influence their immune responses in both the periphery and the brain. We orally administered a broad-spectrum antibiotic (ABX) cocktail consisting of vancomycin 0.5 mg/mL, ampicillin 1 mg/mL, and neomycin 1 mg/mL to pregnant dams during late gestation through birth. Bacterial DNA was extracted from offspring fecal samples, and 16S ribosomal RNA gene was sequenced by Illumina, followed by analysis of gut microbiota composition and PICRUSt prediction. Serum and brain tissue cytokine levels were analyzed by Luminex. Our results indicate that the ABX-cocktail led to significant diversity and taxonomic changes to the offspring’s gut microbiome. In addition, the predicted KEGG and MetaCyc pathways were significantly altered in the offspring. Finally, there were decreased innate inflammatory cytokines and chemokines and interleukin (IL)-17 seen in the brains of ABX-cocktail offspring in response to lipopolysaccharide (LPS) immune challenge. Our results suggest that maternal ABX can produce long-lasting effects on the gut microbiome and neuroimmune responses of offspring. These findings support the role of the early microbiome in the development of offspring gastrointestinal and immune systems.
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Ahmed, Arsalan, Anam Khurshid, Xianghai Tang, Junhao Wang, Tehsin Ullah Khan, and Yunxiang Mao. "Structural and Functional Impacts of Microbiota on Pyropia yezoensis and Surrounding Seawater in Cultivation Farms along Coastal Areas of the Yellow Sea." Microorganisms 9, no. 6 (June 12, 2021): 1291. http://dx.doi.org/10.3390/microorganisms9061291.
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Pyropia yezoensis is the most important commercial edible red algae in China, carrying a variety of resident microbes at its surface. To understand microbiome diversity, community structure, interactions and functions with hosts in this regard, thalli and seawater sampleswere collected from Yantai and Rizhao cultivation farms in the Yellow Sea. The thalli and seawater samples (n = 12) were collected and studied using an Illumina NovaSeq 6000 platform and 16S ribosomal RNA (rRNA) gene sequencing, along with the consideration of environmental factors. Bacterial communities in association with P. yezoensis and surrounding seawater were predominated by Cyanobacteria, Proteobacteria, and Bacteroidetes. The variability of bacterial communities related to P. yezoensis and seawater were predominantly shaped by nitrate (NO3), ammonium (NH4), and temperature. Cluster analysis revealed a close relationship between thalli (RTH and YTH) and seawater (RSW and YSW) in terms of the residing bacterial communities, respectively. PICRUSt analysis revealed the presence of genes associated with amino acid transportation and metabolism, which explained the bacterial dependence on algal-provided nutrients. This study reveals that the diversity of microbiota for P. yezoensis is greatly influenced by abiotic factors and algal organic exudates which trigger chemical signaling and transportation responses from the bacterial community, which in turn activates genes to metabolize subsequent substrates.
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Esberg, Anders, Linda Johansson, Ingegerd Johansson, and Solbritt Rantapää Dahlqvist. "Oral Microbiota Identifies Patients in Early Onset Rheumatoid Arthritis." Microorganisms 9, no. 8 (August 3, 2021): 1657. http://dx.doi.org/10.3390/microorganisms9081657.
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Rheumatoid arthritis (RA) is the most common autoimmune inflammatory disease, and single periodontitis-associated bacteria have been suggested in disease manifestation. Here, the oral microbiota was characterized in relation to the early onset of RA (eRA) taking periodontal status into consideration. 16S rRNA gene amplicon sequencing of saliva bacterial DNA from 61 eRA patients without disease-modifying anti-rheumatic drugs and 59 matched controls was performed. Taxonomic classification at 98.5% was conducted against the Human Oral Microbiome Database, microbiota functions were predicted using PICRUSt, and periodontal status linked from the Swedish quality register for clinically assessed caries and periodontitis. The participants were classified into three distinct microbiota-based cluster groups with cluster allocation differences by eRA status. Independently of periodontal status, eRA patients had enriched levels of Prevotella pleuritidis, Treponema denticola, Porphyromonas endodontalis and Filifactor alocis species and in the Porphyromonas and Fusobacterium genera and functions linked to ornithine metabolism, glucosylceramidase, beta-lactamase resistance, biphenyl degradation, fatty acid metabolism and 17-beta-estradiol-17-dehydrogenase metabolism. The results support a deviating oral microbiota composition already in eRA patients compared with healthy controls and highlight a panel of oral bacteria that may be useful in eRA risk assessment in both periodontally healthy and diseased persons.
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Chigwada, Aubrey Dickson, Ntanganedzeni Olivia Mapholi, Henry Joseph Oduor Ogola, Sikhumbuzo Mbizeni, and Tracy Madimabi Masebe. "Pathogenic and Endosymbiotic Bacteria and Their Associated Antibiotic Resistance Biomarkers in Amblyomma and Hyalomma Ticks Infesting Nguni Cattle (Bos spp.)." Pathogens 11, no. 4 (April 2, 2022): 432. http://dx.doi.org/10.3390/pathogens11040432.
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Deciphering the interactions between ticks and their microbiome is key to revealing new insights on tick biology and pathogen transmission. However, knowledge on tick-borne microbiome diversity and their contribution to drug resistance is scarce in sub–Saharan Africa (SSA), despite endemism of ticks. In this study, high-throughput 16S rRNA amplicon sequencing and PICRUSt predictive function profiling were used to characterize the bacterial community structure and associated antibiotic resistance markers in Amblyomma variegatum, A. hebraeum, and Hyalomma truncatum ticks infesting Nguni cattle (Bos spp.). Twenty-one (seven families and fourteen genera) potentially pathogenic and endosymbiotic bacterial taxa were differentially enriched in two tick genera. In H. truncatum ticks, a higher abundance of Corynebacterium (35.6%), Porphyromonas (14.4%), Anaerococcus (11.1%), Trueperella (3.7%), and Helcococcus (4.7%) was detected. However, Rickettsia (38.6%), Escherichia (7%), and Coxiellaceae (2%) were the major differentially abundant taxa in A. variegatum and A. hebraeum. Further, an abundance of 50 distinct antibiotic resistance biomarkers relating to multidrug resistance (MDR) efflux pumps, drug detoxification enzymes, ribosomal protection proteins, and secretion systems, were inferred in the microbiome. This study provides theoretical insights on the microbiome and associated antibiotic resistance markers, important for the design of effective therapeutic and control decisions for tick-borne diseases in the SSA region.
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Sivaram, Anithadevi Kenday, Logeshwaran Panneerselvan, Kannappar Mukunthan, and Mallavarapu Megharaj. "Effect of Pyroligneous Acid on the Microbial Community Composition and Plant Growth-Promoting Bacteria (PGPB) in Soils." Soil Systems 6, no. 1 (January 14, 2022): 10. http://dx.doi.org/10.3390/soilsystems6010010.
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Pyroligneous acid (PA) is often used in agriculture as a plant growth and yield enhancer. However, the influence of PA application on soil microorganisms is not often studied. Therefore, in this study, we investigated the effect of PA (0.01–5% w/w in soil) on the microbial diversity in two different soils. At the end of eight weeks of incubation, soil microbial community dynamics were determined by Illumina-MiSeq sequencing of 16S rRNA gene amplicons. The microbial composition differed between the lower (0.01% and 0.1%) and the higher (1% and 5%) concentration in both PA spiked soils. The lower concentration of PA resulted in higher microbial diversity and dehydrogenase activity (DHA) compared to the un-spiked control and the soil spiked with high PA concentrations. Interestingly, PA-induced plant growth-promoting bacterial (PGPB) genera include Bradyrhizobium, Azospirillum, Pseudomonas, Mesorhizobium, Rhizobium, Herbaspiriluum, Acetobacter, Beijerinckia, and Nitrosomonas at lower concentrations. Additionally, the PICRUSt functional analysis revealed the predominance of metabolism as the functional module’s primary component in both soils spiked with 0.01% and 0.1% PA. Overall, the results elucidated that PA application in soil at lower concentrations promoted soil DHA and microbial enrichment, particularly the PGPB genera, and thus have great implications for improving soil health.