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Journal articles on the topic 'Patescibacteria'

Author: Grafiati

Published: 7 July 2024

Last updated: 31 July 2025

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1

Hosokawa, Suguru, Kyohei Kuroda, Takashi Narihiro, et al. "Cometabolism of the Superphylum Patescibacteria with Anammox Bacteria in a Long-Term Freshwater Anammox Column Reactor." Water 13, no. 2 (2021): 208. http://dx.doi.org/10.3390/w13020208.

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Although the anaerobic ammonium oxidation (anammox) process has attracted attention regarding its application in ammonia wastewater treatment based on its efficiency, the physiological characteristics of anammox bacteria remain unclear because of the lack of pure-culture representatives. The coexistence of heterotrophic bacteria has often been observed in anammox reactors, even in those fed with synthetic inorganic nutrient medium. In this study, we recovered 37 draft genome bins from a long-term-operated anammox column reactor and predicted the metabolic pathway of coexisting bacteria, especi

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Rahlff, Janina, Helge-Ansgar Giebel, Christian Stolle, Oliver Wurl, Alexander J. Probst, and Daniel P. R. Herlemann. "Overlooked Diversity of Ultramicrobacterial Minorities at the Air-Sea Interface." Atmosphere 11, no. 11 (2020): 1214. http://dx.doi.org/10.3390/atmos11111214.

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Members of the Candidate phylum Patescibacteria, also called Candidate Phyla Radiation (CPR), are described as ultramicrobacteria with limited metabolic capacities. Wide diversity and relative abundances up to 80% in anaerobic habitats, e.g., in groundwater or sediments are characteristic for Candidatus Patescibacteria. However, only few studies exist for marine surface water. Here, we report the presence of 40 patescibacterial candidate clades at air-sea interfaces, including the upper water layer, floating foams and the sea-surface microlayer (SML), a < 1 mm layer at the boundary between

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Liang, Hai-Yan, Yanru Wang, Xiaoqiang Quan, et al. "Ammonium and Nitrate Nitrogen Alter Bacterial Community in the Rhizospheres and Root Surfaces with Seedling Growth of Two Tree Species." Forests 15, no. 12 (2024): 2218. https://doi.org/10.3390/f15122218.

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Ammonium nitrogen (NH4+-N) and nitrate nitrogen (NO3−-N) that can be absorbed and utilized by plants are heterogeneously distributed in soil, which affects plant growth and bacterial communities in the roots. To investigate the effects of single and mixed nitrogen (N) on bacterial communities in the rhizospheres and root surfaces of Cunninghamia lanceolata (CR, CRS) and Schima superba (SR, SRS), we subjected three different ratios of NH4+-N to NO3−-N 2:0, 1:1 (control, CK), 0:2 to cultivate the seedlings. Compared with the CK, the ratio of 0:2 increased the number, diversity, and composition o

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Frunze, Nina. "Soil prokaryotes - an important component of soil and a sensitive index of its health." Studia Universitatis Moldaviae. Seria Științe ale Naturii, no. 1(181) (June 2025): 90–98. https://doi.org/10.59295/sum1(181)2025_12.

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It was established that the spectrum of prokaryotic communities of the studied chernozem is formed by 15 phyla: Pseudomonadota, Actinomycetota, Nitrosophaerota, Bacteroidota, Bacillota, Acidobacteriota, Verrucomicrobiota, Myxococcota and Cyanobacteria, Gemmatimonadota, Nitrospirota Patescibacteria, Planctomycetota, Chloroflexota and Fibrobacterota, 14 of which are representatives of the Bacteria domain (91.85-88.37%) and one, Nitrosophaerota - representative of the Archaea domain (8.15-11.63%). Little-studied, but potentially present in soil since the beginning of time, representatives of the

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Sánchez-Osuna, Miquel, Jordi Barbé, and Ivan Erill. "Comparative genomics of the DNA damage-inducible network in the Patescibacteria." Environmental Microbiology 19, no. 9 (2017): 3465–74. http://dx.doi.org/10.1111/1462-2920.13826.

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Jin, Yuqin, Shunlong Meng, Huimin Xu, et al. "Characteristics of Water Environment and Intestinal Microbial Community of Largemouth Bass (Micropterus salmoides) Cultured Under Biofloc Model." Microorganisms 12, no. 11 (2024): 2158. http://dx.doi.org/10.3390/microorganisms12112158.

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To investigate the effects of biofloc mode on the water environment and intestinal microbial community structure of largemouth bass, a 60-day culture experiment was conducted without water replacement in 300-L glass tanks. The experiment included a control group and a biofloc group, each with three replicates. The results showed the following: (i) the richness and diversity of the water environment and fish intestinal microbial community increased under the biofloc model; (ii) Proteobacteria, Patescibacteria, and Bacteroidota were the dominant phyla in the water environment of largemouth bass,

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La Cono, Violetta, Gina La Spada, Francesco Smedile, et al. "Unique Features of Extremely Halophilic Microbiota Inhabiting Solar Saltworks Fields of Vietnam." Microorganisms 12, no. 10 (2024): 1975. http://dx.doi.org/10.3390/microorganisms12101975.

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The artificial solar saltworks fields of Hon Khoi are important industrial and biodiversity resources in southern Vietnam. Most hypersaline environments in this area are characterized by saturated salinity, nearly neutral pH, intense ultraviolet radiation, elevated temperatures and fast desiccation processes. However, the extremely halophilic prokaryotic communities associated with these stressful environments remain uninvestigated. To fill this gap, a metabarcoding approach was conducted to characterize these communities by comparing them with solar salterns in northern Vietnam as well as wit

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Lemos, Leandro, Lokeshwaran Manoharan, Lucas Mendes, Andressa Venturini, Victor Pylro, and Siu Mui Tsai. "Metagenome assembled‐genomes reveal similar functional profiles of CPR /Patescibacteria phyla in soils." Environmental Microbiology Reports 12, no. 6 (2020): 651–55. http://dx.doi.org/10.1111/1758-2229.12880.

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9

Hernandez, Abbi, Sara Burke, Thomas Buford, and Christy Carter. "Influence of aging, macronutrient composition and time-restricted feeding on the rat gut microbiome." Innovation in Aging 4, Supplement_1 (2020): 888. http://dx.doi.org/10.1093/geroni/igaa057.3278.

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Abstract Declining health and cognition are hallmarks of advanced age that reduce both the quality and length of the lifespan. While caloric restriction has been highlighted as a strategy for increasing healthspan, time-restricted feeding and changes in dietary macronutrient composition may be more feasible alternatives with similar health outcomes. Furthermore, age-related changes in gut microbiome composition may reciprocally interact with several physiological systems – providing a good target for future therapeutic interventions. To begin to investigate the potential utility of a ketogenic

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Hernandez, Shane R., Alexander M. Stelzleni, Wil Sims, Dylan B. Davis, Jeferson M. Lourenco, and R. Lawton Stewart. "2 Measuring the Impact of Heat Stress Abatement Strategies on Fecal Microbiome in Finishing Steers During the Summer Months in the Southeast United States." Journal of Animal Science 99, Supplement_3 (2021): 4–5. http://dx.doi.org/10.1093/jas/skab235.007.

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Abstract This study evaluated the effect of heat stress abatement strategies on the faecal microbiome of finishing beef steers in the Southeastern United States. The study was designed as a completely randomized block using 32 steers (BW 453k 4 kg) stratified by weight and randomly assigned to one of four treatment groups: covered with fans (CWF), covered no fans (CNF), outside with shade (SHADE), and outside without shade (OUT). All steers were housed outside from June to July and were brought up on a common feedlot ration. After-which steers were placed into treatments on d -10 and covered s

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Zhu, Hong, Houwen Zhang, Bonan Hou, Bin Xu, Liting Ji, and You Wu. "Curcumin Regulates Gut Microbiota and Exerts a Neuroprotective Effect in the MPTP Model of Parkinson’s Disease." Evidence-Based Complementary and Alternative Medicine 2022 (November 24, 2022): 1–16. http://dx.doi.org/10.1155/2022/9110560.

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Objectives. The experiment aimed to explore the effects of curcumin on motor impairment, dopamine neurons, and gut microbiota in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mice model. Methods. Mice were randomly assigned to six groups: normal control group, solvent control group, MPTP group, curcumin-low-dose group (40 mg/kg), curcumin-medium-dose group (80 mg/kg), and curcumin-high-dose group (160 mg/kg). After 14 days, each group of mice was subjected to the pole text, the hanging test, and the open-field test. Tyrosine hydroxylase (TH) immunohistochemistry was used to observe t

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Fu, Haiyan, Dapeng Song, Kunpeng Wang, et al. "Application of Wheat Straw Compost Mixed with Chemical Fertilizer Regulates Soil Bacterial Community Diversity in Tea (Camellia sinensis) Plantation." Diversity 15, no. 4 (2023): 580. http://dx.doi.org/10.3390/d15040580.

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Biofertilizers have been suggested as alternatives to synthetic fertilizers, which could reduce soil degradation brought on by excessive chemical fertilization and have an impact on the bacterial diversity and community in the soil. The diversity and community of soil bacteria in tea plantations treated with wheat straw compost have, however, received relatively little attention. In this research, a two-year field trial was run to examine the effects of applying wheat straw compost on the characteristics of the soil and the quality of the tea. We also used high-throughput sequencing to investi

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Lemos, Leandro N., Julliane D. Medeiros, Francisco Dini‐Andreote, et al. "Genomic signatures and co‐occurrence patterns of the ultra‐small Saccharimonadia (phylum CPR/Patescibacteria) suggest a symbiotic lifestyle." Molecular Ecology 28, no. 18 (2019): 4259–71. http://dx.doi.org/10.1111/mec.15208.

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14

Wang, Weihan, Dandan Zhang, Hao Kong, Gengtao Zhang, Feng Shen, and Zhiping Huang. "Effects of Salinity Accumulation on Physical, Chemical, and Microbial Properties of Soil under Rural Domestic Sewage Irrigation." Agronomy 14, no. 3 (2024): 514. http://dx.doi.org/10.3390/agronomy14030514.

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Under irrigation with saline wastewater, SO42−, Cl−, and Ca2+ aggregated in the topsoil, and Mg2+ was significantly higher in the deeper soil than in the topsoil and 40 cm soil layers. The abundance of Zoopagomycota, Ascomycota, Mortierellomycota, Basidiomycota, Chytridiomycota, Rozellomycota, Blastocladiomycota, Monoblepharomycota, Mucoromycota and Olpidiomycota in the surface soil was influenced by Mg2+, whereas Ca2+ affected the abundance of Zoopagomycota and Chytridiomycota. In the 40 cm soil layer, Mg2+ and Cl− promoted Actinobacteria, Proteobacteria, Nitrospirae, Firmicutes, Entotheonell

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15

Smedile, Francesco, Cono Violetta La, Stefano Urbano, et al. "The perennially ice-covered Lake Enigma, Antarctica supports unique microbial communities." Communications Earth & Environment 5 (November 3, 2024): 741. https://doi.org/10.1038/s43247-024-01842-5.

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Northern Foothills of Victoria Land, Antarctica contains numerous hydrological formations, rangingfrom small surface streams and ponds fed by glacial or snow meltwater to permafrost lakes containingbriny pockets. Here we describe the discovery of a massive body of unfrozen stratified oligotrophicwater in Lake Enigma, a permanently ice-covered lake previously thought to be frozen from top tobottom. A remarkable feature of the Lake Enigma microbial ecosystem is the presence, andsometimes even dominance, of ultrasmall bacteria belonging to the superphylum Patescibacteria, agroup apparently absent

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Kagemasa, Shuka, Kyohei Kuroda, Ryosuke Nakai, Yu-You Li, and Kengo Kubota. "Diversity of <i>Candidatus</i> Patescibacteria in Activated Sludge Revealed by a Size-‍Fractionation Approach." Microbes and Environments 37, no. 2 (2022): n/a. http://dx.doi.org/10.1264/jsme2.me22027.

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Yang, Yehua, Xingcheng Huang, Huaqing Zhu, et al. "Characteristics of Bacterial Community Structure in Yellow Paddy Soil After Long-Term Chemical Fertilisation, Organic Fertilisation, and Fertilisation Mode Conversion." Agronomy 15, no. 3 (2025): 749. https://doi.org/10.3390/agronomy15030749.

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This study aimed to compare bacterial community structure differences in yellow paddy soil under long-term chemical/organic fertilisation and fertiliser conversion to guide farmland fertilisation strategies in yellow loam areas. Treatments included (1) continuous application of chemical fertilisers for 27 years (CF-CF); (2) application of chemical fertiliser continuously for 24 years and then application of organic fertiliser for 3 years (CF-OF); (3) continuous application of organic fertiliser for 27 years (OF-OF); and (4) application of organic fertiliser continuously for 24 years and then a

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18

Liu, Bin, Zhenghua Ding, Junhui Xiong, Xing Heng, Huafu Wang, and Weihua Chu. "Gut Microbiota and Inflammatory Cytokine Changes in Patients with Ankylosing Spondylitis." BioMed Research International 2022 (August 19, 2022): 1–6. http://dx.doi.org/10.1155/2022/1005111.

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Ankylosing spondylitis (AS) is a chronic inflammatory disease characterized by sacroiliac joint lesions and spinal ascending involvement. The aim of this work was at investigating the gut microbiota profile and proinflammatory cytokines in AS patients. Gut microbiota of AS patients was clearly different from that of healthy human controls. 16S rRNA sequencing analysis demonstrated a changed microbial diversity in the AS patients, and there was a significant increase in the abundance of Cyanobacteria, Deinococcota, Patescibacteria, Actinobacteriota, and Synergistota at a phyla level increased i

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Gu, Yaqiong, Beiying Li, Xiang Zhong, Conghe Liu, and Bin Ma. "Bacterial Community Composition and Function in a Tropical Municipal Wastewater Treatment Plant." Water 14, no. 10 (2022): 1537. http://dx.doi.org/10.3390/w14101537.

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Bacterial diversity and community composition are of great importance in wastewater treatment; however, little is known about the diversity and community structure of bacteria in tropical municipal wastewater treatment plants (WWTPs). Therefore, in this study, activated sludge samples were collected from the return sludge, anaerobic sludge, anoxic sludge, and aerobic sludge of an A2O WWTP in Haikou, China. Illumina MiSeq high-throughput sequencing was used to examine the 16S ribosomal RNA (rRNA) of bacteria in the samples. The microbial community diversity in this tropical WWTP was higher than

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Alqaderi, Hend, Meganathan P. Ramakodi, Rasheeba Nizam, et al. "Salivary Microbiome Diversity in Kuwaiti Adolescents with Varied Body Mass Index—A Pilot Study." Microorganisms 9, no. 6 (2021): 1222. http://dx.doi.org/10.3390/microorganisms9061222.

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The potential role of the salivary microbiome in human diseases has increasingly been explored. The salivary microbiome has been characterized in several global populations, except the Arabian Gulf region. Hence, in this pilot study, we profiled the salivary microbiome of Kuwaiti adolescents with varied body mass indexes (BMI). The analyses of core microbiome composition showed Firmicutes, Bacteroidota, Proteobacteria, Patescibacteria, Fusobacteriota, Actinobacteriota, and Campylobacterota as the common phylum found in the Kuwaiti adolescent population. We also illustrated a diverse microbial

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Yi, Xin, Baoyun Wu, Jinglei Ma, et al. "Effects of Dietary Capsaicin and Yucca schidigera Extracts as Feed Additives on Rumen Fermentation and Microflora of Beef Cattle Fed with a Moderate-Energy Diet." Fermentation 9, no. 1 (2022): 30. http://dx.doi.org/10.3390/fermentation9010030.

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Capsaicin (CAP) and Yucca schidigera extract (YSE) are two types of plant extracts that can change rumen fermentation. This study was conducted to investigate whether supplementation of beef cattle diets with CAP and YSE for 90 days would affect rumen fermentation and microflora. Forty-five healthy Angus steers (initial body weight = 510.54 ± 41.27 kg) were divided into three groups: control (CON), CAP, and YSE. Ammonia nitrogen (NH3-N) and total volatile fatty acid (TVFA) concentrations were significantly higher in the YSE group than in the CON group and significantly lower in the CAP group t

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Zhao, Z., S. Yu, X. Han, and S. Yang. "Influence of drought and dry-wet alternation on nitrogen transformation and low abundance microorganisms in tea garden soil." Journal of Environmental Biology 43, no. 2 (2022): 231–38. http://dx.doi.org/10.22438/jeb/43/2/mrn-2068.

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Aim: The soil water availability seriously limits the growth and development of tea plants, and soil microorganisms are an important medium to regulate soil nutrient cycling. In this study, the effects of water supply mode on soil nitrogen nutrition and soil microbes in tea gardens were investigated. Methodology: This experiment set up consisted two water supply modes (consecutive drought and dry-wet alternation) by using the soil microcosm incubation experiment, and four treatments were set: 20% water holding capacity for 21day (D21); 20% water holding capacity for 1-7 days and 60% water hold

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Bayer, Kristina, Kathrin Busch, Ellen Kenchington, et al. "Microbial strategies for survival in the glass sponge Vazella pourtalesii." mSystems 5 (August 11, 2020): e00473-20. https://doi.org/10.1128/mSystems.00473-20.

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ABSTRACT. Few studies have explored the microbiomes of glass sponges (Hexactinellida). The present study seeks to elucidate the composition of the microbiota associated with the glass sponge <em>Vazella pourtalesii </em>and the functional strategies of the main symbionts. We combined microscopic approaches with metagenome-guided microbial genome reconstruction and amplicon community profiling toward this goal. Microscopic imaging revealed that the host and microbial cells appeared within dense biomass patches that are presumably syncytial tissue aggregates. Based on abundances in amplicon libr

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Frunze, Nina. "COMPONENȚA TAXONOMICĂ A COMUNITĂȚILOR PROCARIOTE DIN CERNOZIOMUL TIPIC ȘI ABUNDENȚA LOR LA NIVEL DE FILUM." AGRICULTURAL SCIENCE, no. 2 (February 5, 2025): 7–16. https://doi.org/10.55505/sa.2024.2.01.

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In the present study, the changes in the taxonomic composition of prokaryotes at the phylum level in the typical chernozem of the Republic of Moldova during the years 2020-2022 were determined, using the polymerase chain reaction (PCR). The group of microorganisms studied is characterized by a genetic diversity, whose spectrum comprises 15 phyla with a different prevalence in the prokaryotic community. The majority (14) belong to the Bacteria domain: Bacteria: Proteobacteria, Actinobacteriota, Bacteroidota, Firmicutes, Verrucomicrobiota, Acidobacteriota, Planctomycetota, Myxococcota, Nitrospir

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Sonthiphand, Prinpida, Pasunun Rattanaroongrot, Kasarnchon Mek-yong, et al. "Microbial community structure in aquifers associated with arsenic: analysis of 16S rRNA and arsenite oxidase genes." PeerJ 9 (January 8, 2021): e10653. http://dx.doi.org/10.7717/peerj.10653.

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The microbiomes of deep and shallow aquifers located in an agricultural area, impacted by an old tin mine, were explored to understand spatial variation in microbial community structures and identify environmental factors influencing microbial distribution patterns through the analysis of 16S rRNA and aioA genes. Although Proteobacteria, Cyanobacteria, Actinobacteria, Patescibacteria, Bacteroidetes, and Epsilonbacteraeota were widespread across the analyzed aquifers, the dominant taxa found in each aquifer were unique. The co-dominance of Burkholderiaceae and Gallionellaceae potentially contro

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Parihar, Jagdish, Suraj P. Parihar, Prashanth Suravajhala, and Ashima Bagaria. "Spatial Metagenomic Analysis in Understanding the Microbial Diversity of Thar Desert." Biology 11, no. 3 (2022): 461. http://dx.doi.org/10.3390/biology11030461.

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The arid and semi-arid regions of Rajasthan are one of the most extreme biomes of India, possessing diverse microbial communities that exhibit immense biotechnological potential for industries. Herein, we sampled study sites from arid and semi-arid regions of Thar Desert, Rajasthan, India and subjected them to chemical, physical and metagenomics analysis. The microbial diversity was studied using V3–V4 amplicon sequencing of 16S rRNA gene by Illumina MiSeq. Our metagenomic analyses revealed that the sampled sites consist mainly of Proteobacteria (19–31%) followed by unclassified bacteria (5–21

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Sonthiphand, Prinpida, Pasunun Rattanaroongrot, Kasarnchon Mek-yong, et al. "Microbial community structure in aquifers associated with arsenic: analysis of 16S rRNA and arsenite oxidase genes." PeerJ 9 (January 8, 2021): e10653. http://dx.doi.org/10.7717/peerj.10653.

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The microbiomes of deep and shallow aquifers located in an agricultural area, impacted by an old tin mine, were explored to understand spatial variation in microbial community structures and identify environmental factors influencing microbial distribution patterns through the analysis of 16S rRNA and aioA genes. Although Proteobacteria, Cyanobacteria, Actinobacteria, Patescibacteria, Bacteroidetes, and Epsilonbacteraeota were widespread across the analyzed aquifers, the dominant taxa found in each aquifer were unique. The co-dominance of Burkholderiaceae and Gallionellaceae potentially contro

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28

Zhang, Yangbo, Jianan Huang, Yifan Xiong, Xiangna Zhang, Yong Lin, and Zhonghua Liu. "Jasmine Tea Attenuates Chronic Unpredictable Mild Stress-Induced Depressive-like Behavior in Rats via the Gut-Brain Axis." Nutrients 14, no. 1 (2021): 99. http://dx.doi.org/10.3390/nu14010099.

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The number of depressed people has increased worldwide. Dysfunction of the gut microbiota has been closely related to depression. The mechanism by which jasmine tea ameliorates depression via the brain-gut-microbiome (BGM) axis remains unclear. Here, the effects of jasmine tea on rats with depressive-like symptoms via the gut microbiome were investigated. We first established a chronic unpredictable mild stress (CUMS) rat model to induce depressive symptoms and measured the changes in depression-related indicators. Simultaneously, the changes in gut microbiota were investigated by 16S rRNA seq

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Satjarak, Anchittha, Jittra Piapukiew, Wikrom Chanthapatchot, Karnjana Ruen-Pham, and Alisa S. Vangnai. "Hercide Atrazine Alters the Microbiota of the Filametous Green Alga Cladophora sp. Cultured from Thailand." Sains Malaysiana 50, no. 5 (2021): 1255–65. http://dx.doi.org/10.17576/jsm-2021-5005-06.

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The attached green alga Cladophora known to harbor microbiota that play important roles in ecosystem, is one of the most common freshwater filamentous green algae in rivers globally, including those in the northern part of Thailand. These rivers mostly run through agricultural regions where herbicides are heavily used to improve crop quality and quantity. The extensively-used herbicide atrazine persists in soil sediments through transport by surface runoff to rivers. The effect of such herbicide contamination on Cladophora microbiota in Thailand have not been investigated. To acquire this info

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Li, Mengwei, Faizul Hassan, Lijuan Peng, et al. "Mulberry flavonoids modulate rumen bacteria to alter fermentation kinetics in water buffalo." PeerJ 10 (December 14, 2022): e14309. http://dx.doi.org/10.7717/peerj.14309.

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Mulberry flavonoids can modulate the composition of rumen microbiota in ruminants to improve nutrient digestibility, owing to their strong biological activities. This study aimed to explore the effect of mulberry leaf flavonoids (MLF) on rumen bacteria, fermentation kinetics, and metagenomic functional profile in water buffalo. Forty buffaloes (4 ± 1 lactations) with almost same body weight (av. 600 ± 50 Kg) and days in milk (90 ± 20 d) were randomly allocated to four treatments having different levels of MLF: 0 g/d (control), 15 g/d (MLF15), 30 g/d (MLF30), and 45 g/d (MLF45) supplemented in

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Zhou, Zhengyao, Meixia Qi, and Hongping Wang. "Achieving Partial Nitrification via Intermittent Aeration in SBR and Short-Term Effects of Different C/N Ratios on Reactor Performance and Microbial Community Structure." Water 12, no. 12 (2020): 3485. http://dx.doi.org/10.3390/w12123485.

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A sequencing batch reactor (SBR) with an intermittent aeration mode was established to achieve partial nitrification (PN) and the short-term effects of C/N ratios were investigated. Stable nitrite accumulation was achieved after 107 cycles, about 56d, with the average ammonia nitrogen removal efficiency (ARE) and nitrite accumulation rate (NAR) of 96.92% and 82.49%, respectively. When the C/N ratios decreased from 4.64 to 3.87 and 2.32, ARE and NAR still kept a stable and high level. However, when the C/N ratio further decreased to 0.77, nitrite accumulation became fluctuation, and ARE, total

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Zhang, Zhimin, Li Yang, Yang He, Xinmao Luo, Shaokang Zhao, and Xianbo Jia. "Composition of Fecal Microbiota in Grazing and Feedlot Angus Beef Cattle." Animals 11, no. 11 (2021): 3167. http://dx.doi.org/10.3390/ani11113167.

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This study is to investigate the difference in bovine fecal microbiota between grazing and feedlot Angus cattle. Fecal samples were collected from six Angus cattle grazed on grassland and six Angus cattle fed on a feedlot. The fecal bacterial community was analyzed by high-throughput sequencing of 16S rRNA gene. Sequencing of the V3–V4 region totally produced 1,113,170 effective tages that were computationally clustered into 775 operational taxonomic units (OTUs). These 775 OTUs were taxonomically assigned to bacterial 12 phyla, 19 classes, 25 orders, 54 families, 141 genera, and 145 species.

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Ravegnini, Gloria, Bruno Fosso, Viola Di Saverio, et al. "Gastric Adenocarcinomas and Signet-Ring Cell Carcinoma: Unraveling Gastric Cancer Complexity through Microbiome Analysis—Deepening Heterogeneity for a Personalized Therapy." International Journal of Molecular Sciences 21, no. 24 (2020): 9735. http://dx.doi.org/10.3390/ijms21249735.

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Gastric cancer (GC) is the fifth most prevalent cancer worldwide and the third leading cause of global cancer mortality. With the advances of the omic studies, a heterogeneous GC landscape has been revealed, with significant molecular diversity. Given the multifaceted nature of GC, identification of different patient subsets with prognostic and/or predictive outcomes is a key aspect to allow tailoring of specific treatments. Recently, the involvement of the microbiota in gastric carcinogenesis has been described. To deepen this aspect, we compared microbiota composition in signet-ring cell car

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Gutnik, D. I., S. A. Potapov, A. Y. Krasnopeev, et al. "Characterization of Saccharimonadia bacteria in Lakes Baikal and Khubsugul: taxonomic and functional diversity." Limnology and Freshwater Biology, no. 4 (2024): 908–24. http://dx.doi.org/10.31951/2658-3518-2024-a-4-908.

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Ultra-small bacteria are ubiquitous in the environment, but for some time they have remained out of scientific focus. One of the reasons is their small size. Ultramicrobacteria, which are defined as bacteria with a cell size of less than 0.1 µm3, can pass through a filter with a pore size of 0.2 µm. Moreover, there are some difficulties associated with their cultivation. Currently, relatively pure cultures have been obtained, but mostly for dominant phyla. Rare phyla are represented only by single strains. At the same time, ultramicrobacteria are found in a wide range of environments, and thei

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Chen, Yixuan, Sen Wang, Yuru Li, Wanyu Liu, and Zhenchuan Niu. "Response of Bacterial Community Structure and Function in Rhizosphere Soil on the Photosynthesis of Selected Plant Types C3 and C4 under Bis(2,4,6-tribromophenoxy) Ethane Exposure." Agriculture 14, no. 9 (2024): 1637. http://dx.doi.org/10.3390/agriculture14091637.

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This study investigated the response of a bacterial community’s structure and function in the rhizosphere soil of C3 and C4 plants under bis(2,4,6-tribromophenoxy) ethane (BTBPE) exposure. The bacterial community composition was determined using 16S rRNA sequencing, while FAPROTAX and PICRUSt 2 were employed for functional predictions. Results showed significant differences between C3 and C4 plants in terms of bacterial community structure. C3 plants exhibited higher abundances of Proteobacteria, Bacteroidetes at the phylum level and Sphingomicrobium at the genus level, compared to C4 plants.

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Wieczorek, Robert, Zofia Zydlik, Agnieszka Wolna-Maruwka, Alicja Niewiadomska, and Dariusz Kayzer. "The Effect of Biofumigation on the Microbiome Composition in Replanted Soil in a Fruit Tree Nursery." Agronomy 13, no. 10 (2023): 2507. http://dx.doi.org/10.3390/agronomy13102507.

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The imbalance of the soil microbiome is a primary indicator of ARD (apple replant disease). Biofumigation is a treatment that enables the restoration of microbiome balance. This study involved an analysis of the taxonomic and functional diversity of bacterial communities in replanted soil (ARD), in replanted soils with forecrops of French marigold (Tagetes patula L.), white mustard (Sinapis alba), and oilseed radish (Raphanus sativus var. oleifera), and in agricultural soil. The biofumigation treatment with phytosanitary plants changed the structure and abundance of the replanted soil microbio

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Cataruci, Amalia C. S., Dione Kawamoto, Natali Shimabukuro, et al. "Oral Administration of Lactobacillus acidophilus LA5 Prevents Alveolar Bone Loss and Alters Oral and Gut Microbiomes in a Murine Periodontitis Experimental Model." Microorganisms 12, no. 6 (2024): 1057. http://dx.doi.org/10.3390/microorganisms12061057.

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Periodontitis is a destructive inflammatory response triggered by dysbiosis. Lactobacillus acidophilus LA5 (LA5) may impair microbial colonization and alter the host. Thus, we evaluated the effect of LA5 on alveolar bone loss in a periodontitis murine model and investigated its effect on the oral and gut microbiomes. Porphyromonas gingivalis, Prevotella intermedia, Fusobacterium nucleatum, and Streptococcus gordonii were inoculated in C57BL/6 mice (P+), with LA5 (L+). SHAM infected controls (P- and/or L- groups) were also evaluated. After 45 days, alveolar bone loss in the maxilla and oral and

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Naccache, Chahnez, Chourouk Ibrahim, Abdennaceur Hassen, and Maha Mezghani Khemakhem. "Metagenomics-based analysis of mobile genetic elements and antibiotic/metal resistance genes carried by treated wastewater." PeerJ 13 (July 23, 2025): e19682. https://doi.org/10.7717/peerj.19682.

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Wastewater treatment plants in Tunisia are recognized as key locations for the spread of antibiotic and heavy metal resistance genes among bacteria. Despite the widespread presence of pollutants in these treatment systems, there is still a significant gap in our understanding of resistance dynamics. This study focused on analyzing the bacterial community and resistome-mobilome profiles of the Charguia wastewater treatment plant (WWTP). Using metagenomics sequencing, six samples from the influent, sludge, and effluent were thoroughly examined. Our research findings indicated the prevalence of P

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Fujii, Naoki, Kyohei Kuroda, Takashi Narihiro, et al. "Metabolic Potential of the Superphylum <i>Patescibacteria</i> Reconstructed from Activated Sludge Samples from a Municipal Wastewater Treatment Plant." Microbes and Environments 37, no. 3 (2022): n/a. http://dx.doi.org/10.1264/jsme2.me22012.

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Cui, Guojie, Jun Li, Zhaoming Gao, and Yong Wang. "Spatial variations of microbial communities in abyssal and hadal sediments across the Challenger Deep." PeerJ 7 (May 17, 2019): e6961. http://dx.doi.org/10.7717/peerj.6961.

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Microbial communities in hadal sediments are least explored in hadal zone (>6,000 m), especially in the Challenger Deep with high pressure (∼110 M pa at the bottom). In this study, we investigated the microbial communities in the sediments of the slope and trench-axis bottom of the Challenger Deep in the Mariana Trench. Classification of the reads of the 16S rRNA gene amplicons showed vertical distribution of prokaryotic microbial inhabitants from the surface to up to 60 centimeter below surface floor (cmbsf). The most dominant phyla were Proteobacteria, Chloroflexi, Actinobacteria, Plancto

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Zhu, Zheng, Xiaoxi Ma, Jie Wu, et al. "Altered Gut Microbiota and Its Clinical Relevance in Mild Cognitive Impairment and Alzheimer’s Disease: Shanghai Aging Study and Shanghai Memory Study." Nutrients 14, no. 19 (2022): 3959. http://dx.doi.org/10.3390/nu14193959.

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Altered gut microbiota has been reported in individuals with mild cognitive impairment (MCI) and Alzheimer’s disease (AD). Previous research has suggested that specific bacterial species might be associated with the decline of cognitive function. However, the evidence was insufficient, and the results were inconsistent. To determine whether there is an alteration of gut microbiota in patients with MCI and AD and to investigate its correlation with clinical characteristics, the fecal samples from 94 cognitively normal controls (NC), 125 participants with MCI, and 83 patients with AD were collec

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Ramdat, Naven, Zi-Jing Wang, Jung-Chen Huang, et al. "Effects of Enrofloxacin on Nutrient Removal by a Floating Treatment Wetland Planted with Iris pseudacorus: Response and Resilience of Rhizosphere Microbial Communities." Sustainability 14, no. 6 (2022): 3358. http://dx.doi.org/10.3390/su14063358.

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Constructed wetlands (CWs), including floating treatment wetlands (FTWs), possess great potential for treating excessive nutrients in surface waters, where, however, the ubiquitous presence of antibiotics, e.g., enrofloxacin (ENR), is threatening the performance of CWs. In developing a more efficient and resilient system, we explored the responses of the FTW to ENR, using tank 1, repeatedly exposed to ENR, and tank 2 as control. Plant growth and nutrient uptake were remarkably enhanced in tank 1, and similar phosphorus removal rates (86~89% of the total added P) were obtained for both tanks ov

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Ivanova, Anastasia A., Alexey V. Beletsky, Andrey L. Rakitin, et al. "Closely Located but Totally Distinct: Highly Contrasting Prokaryotic Diversity Patterns in Raised Bogs and Eutrophic Fens." Microorganisms 8, no. 4 (2020): 484. http://dx.doi.org/10.3390/microorganisms8040484.

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Large areas in Northern Russia are covered by extensive mires, which represent a complex mosaic of ombrotrophic raised bogs, minerotrophic and eutrophic fens, all in a close proximity to each other. In this paper, we compared microbial diversity patterns in the surface peat layers of the neighbouring raised bogs and eutrophic fens that are located within two geographically remote mire sites in Vologda region using 16S rRNA gene sequencing. Regardless of location, the microbial communities in raised bogs were highly similar to each other but were clearly distinct from those in eutrophic fens. B

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Ujvári, Gergely, Andrea K. Borsodi, Melinda Megyes, et al. "Comparison of Soil Bacterial Communities from Juvenile Maize Plants of a Long-Term Monoculture and a Natural Grassland." Agronomy 10, no. 3 (2020): 341. http://dx.doi.org/10.3390/agronomy10030341.

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Nowadays, one of the most important challenges is to ensure sustainable agricultural management of crops such as maize (Zea mays L.). Long-term crop production, however, may influence the soil properties, the composition and activity of microbial communities. The aim of this study was to compare the catabolic activity and taxonomic diversity of bacterial communities inhabiting the soil of a non-fertilized maize monoculture and a natural grassland. Samples were taken from the horizons A and C in the first part of the vegetation period. MicroResp™ technique was used to explore the catabolic pote

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Ge, Liqiang, Xin Yuan, Longlong Zhang, Hang Li, Xiaoyu Liu, and Xiaohua Zhu. "Uncovering the Relationship Between Soil Bacterial Community and Heavy Metals in a Copper Waste Pile." Minerals 14, no. 12 (2024): 1237. https://doi.org/10.3390/min14121237.

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In the present study, the relationship between the microbial community and heavy metal content of soil was analyzed based on 16S rRNA gene high-throughput sequencing, in order to screen the corresponding heavy metal-resistant bacteria in a copper mine waste dump and adjacent shrubbery. Approximately 22 phyla, 57 classes, 128 orders, 173 families, 263 genera, 433 species, and 954 OUTs obtained from soil sample species annotation indicated the Spearman relevance analysis at the phylum level. Specifically, Gemmatimonadota is positively correlated with arsenic (As); Patescibacteria is positively c

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Ozer, Hasan, Naime Ozdemir, Asude Ates, Rabia Koklu, Sinem Ozturk Erdem, and Saim Ozdemir. "Circular Utilization of Coffee Grounds as a Bio-Nutrient through Microbial Transformation for Leafy Vegetables." Life 14, no. 10 (2024): 1299. http://dx.doi.org/10.3390/life14101299.

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This study explores the production of bio-nutrients from bioactive compound-rich spent coffee grounds (SCG) and biochar (BC) through composting after inoculation with a biological agent and its impact on the growth performance of garden cress and spinach. The SCG was composted with six doses of BC (0, 5, 10, 15, 20, and 25%). The compost with 10% BC exhibited the best maturity, humification, and phytotoxicity index values of dissolved organic carbon (DOC), humification index (E4/E6), and germination index (GI). A metagenome analysis showed that compost starter enhanced the bacterial community’

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Coelho, Catarina, Igor Tiago, and António Veríssimo. "Guts Bacterial Communities of Porcellio dilatatus: Symbionts Predominance, Functional Significance and Putative Biotechnological Potential." Microorganisms 10, no. 11 (2022): 2230. http://dx.doi.org/10.3390/microorganisms10112230.

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Terrestrial isopods are effective herbivorous scavengers with an important ecological role in organic matter cycling. Their guts are considered to be a natural enrichment environment for lignocellulosic biomass (LCB)-degrading bacteria. The main goal of this work was to assess the structural diversity of Porcellio dilatatus gut bacterial communities using NGS technologies, and to predict their functional potential using PICRUSt2 software. Pseudomonadota, Actinomycetota, Bacillota, Cyanobacteria, Mycoplasmatota, Bacteroidota, Candidatus Patescibacteria and Chloroflexota were the most abundant p

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Dutkiewicz, Zuzanna, Caitlin Margaret Singleton, Mantas Sereika, et al. "Proposal of Patescibacterium danicum gen. Nov., sp. nov. in the ubiquitous ultrasmall bacterial phylum Patescibacteriota phyl. Nov." ISME Communications, November 19, 2024. http://dx.doi.org/10.1093/ismeco/ycae147.

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Abstract Candidatus Patescibacteria is a diverse bacterial phylum that is notable for members with ultrasmall cell size, reduced genomes, limited metabolic capabilities and dependence on other prokaryotic hosts. Despite the prevalence of the name Ca. Patescibacteria in the scientific literature, it is not officially recognized under the International Code of Nomenclature of Prokaryotes (ICNP) and lacks a nomenclatural type. Here, we rectify this situation by describing two closely related circular metagenome-assembled genomes (MAGs) and by proposing one of them (ABY1TS) to serve as the nomencl

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Hu, Huifeng, Jannie Munk Kristensen, Craig William Herbold, et al. "Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants." Microbiome 12, no. 1 (2024). http://dx.doi.org/10.1186/s40168-024-01769-1.

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Abstract Background Microorganisms are responsible for nutrient removal and resource recovery in wastewater treatment plants (WWTPs), and their diversity is often studied by 16S rRNA gene amplicon sequencing. However, this approach underestimates the abundance and diversity of Patescibacteria due to the low coverage of commonly used PCR primers for this highly divergent bacterial phylum. Therefore, our current understanding of the global diversity, distribution, and ecological role of Patescibacteria in WWTPs is very incomplete. This is particularly relevant as Patescibacteria are considered t

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Vigneron, Adrien, Perrine Cruaud, Rémy Guyoneaud, and Marisol Goñi-Urriza. "Into the darkness of the microbial dark matter in situ activities through expression profiles of Patescibacteria populations." Frontiers in Microbiology 13 (January 9, 2023). http://dx.doi.org/10.3389/fmicb.2022.1073483.

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Patescibacteria form a highly diverse and widespread superphylum of uncultured microorganisms representing a third of the global microbial diversity. Most of our knowledge on Patescibacteria putative physiology relies on metagenomic mining and metagenome-assembled genomes, but the in situ activities and the ecophysiology of these microorganisms have been rarely explored, leaving the role of Patescibacteria in ecosystems elusive. Using a genome-centric metatranscriptomic approach, we analyzed the diel and seasonal gene transcription profiles of 18 Patescibacteria populations in brackish microbi

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