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Journal articles on the topic 'Molecular operational taxonomic unit'
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1
Galimberti, Andrea, Martina Spada, Danilo Russo, et al. "Integrated Operational Taxonomic Units (IOTUs) in Echolocating Bats: A Bridge between Molecular and Traditional Taxonomy." PLoS ONE 7, no. 6 (2012): e40122. https://doi.org/10.5281/zenodo.13484858.
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(Uploaded by Plazi for the Bat Literature Project) Background: Nowadays, molecular techniques are widespread tools for the identification of biological entities. However, until very few years ago, their application to taxonomy provoked intense debates between traditional and molecular taxonomists. To prevent every kind of disagreement, it is essential to standardize taxonomic definitions. Along these lines, we introduced the concept of Integrated Operational Taxonomic Unit (IOTU). IOTUs come from the concept of Operational Taxonomic Unit (OTU) and paralleled the Molecular Operational Taxonomic Unit (MOTU). The latter is largely used as a standard in many molecular-based works (even if not always explicitly formalized). However, while MOTUs are assigned solely on molecular variation criteria, IOTUs are identified from patterns of molecular variation that are supported by at least one more taxonomic characteristic. Methodology/Principal Findings: We tested the use of IOTUs on the widest DNA barcoding dataset of Italian echolocating bats species ever assembled (i.e. 31 species, 209 samples). We identified 31 molecular entities, 26 of which corresponded to the morphologically assigned species, two MOTUs and three IOTUs. Interestingly, we found three IOTUs in Myotis nattereri, one of which is a newly described lineage found only in central and southern Italy. In addition, we found a level of molecular variability within four vespertilionid species deserving further analyses. According to our scheme two of them (i.e. M. bechsteinii and Plecotus auritus) should be ranked as unconfirmed candidate species (UCS). Conclusions/Significance: From a systematic point of view, IOTUs are more informative than the general concept of OTUs and the more recent MOTUs. According to information content, IOTUs are closer to species, although it is important to underline that IOTUs are not species. Overall, the use of a more precise panel of taxonomic entities increases the clarity in the systematic field and has the potential to fill the gaps between modern and traditional taxonomy.
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Galimberti, Andrea, Martina Spada, Danilo Russo, et al. "Integrated Operational Taxonomic Units (IOTUs) in Echolocating Bats: A Bridge between Molecular and Traditional Taxonomy." PLoS ONE 7, no. 6 (2012): e40122. https://doi.org/10.5281/zenodo.13484858.
Full textAbstract:
(Uploaded by Plazi for the Bat Literature Project) Background: Nowadays, molecular techniques are widespread tools for the identification of biological entities. However, until very few years ago, their application to taxonomy provoked intense debates between traditional and molecular taxonomists. To prevent every kind of disagreement, it is essential to standardize taxonomic definitions. Along these lines, we introduced the concept of Integrated Operational Taxonomic Unit (IOTU). IOTUs come from the concept of Operational Taxonomic Unit (OTU) and paralleled the Molecular Operational Taxonomic Unit (MOTU). The latter is largely used as a standard in many molecular-based works (even if not always explicitly formalized). However, while MOTUs are assigned solely on molecular variation criteria, IOTUs are identified from patterns of molecular variation that are supported by at least one more taxonomic characteristic. Methodology/Principal Findings: We tested the use of IOTUs on the widest DNA barcoding dataset of Italian echolocating bats species ever assembled (i.e. 31 species, 209 samples). We identified 31 molecular entities, 26 of which corresponded to the morphologically assigned species, two MOTUs and three IOTUs. Interestingly, we found three IOTUs in Myotis nattereri, one of which is a newly described lineage found only in central and southern Italy. In addition, we found a level of molecular variability within four vespertilionid species deserving further analyses. According to our scheme two of them (i.e. M. bechsteinii and Plecotus auritus) should be ranked as unconfirmed candidate species (UCS). Conclusions/Significance: From a systematic point of view, IOTUs are more informative than the general concept of OTUs and the more recent MOTUs. According to information content, IOTUs are closer to species, although it is important to underline that IOTUs are not species. Overall, the use of a more precise panel of taxonomic entities increases the clarity in the systematic field and has the potential to fill the gaps between modern and traditional taxonomy.
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Beck, D., M. Settles, and J. A. Foster. "OTUbase: an R infrastructure package for operational taxonomic unit data." Bioinformatics 27, no. 12 (2011): 1700–1701. http://dx.doi.org/10.1093/bioinformatics/btr196.
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Kharat, Milindkumar M., Santosh G. Atram, Vikas M. Kothare, and Pranav T. Bhoyar. "COI gene variability in Wallago attu and its close related species Ompok bimaculatus." International Journal of Advance and Applied Research 5, no. 23 (2024): 405–12. https://doi.org/10.5281/zenodo.13637687.
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<strong>Abstract:</strong> Taxonomy based of Cytochrome Oxidase 1 Gene is a novel technique in the field of animal identification. DNA sequences to be aligned for the taxonomic process are aligned in software MEGA. Alignment of different sequences world over for the fish <em>Wallago attu </em>have been worked out in the present study with its taxonomically close individual <em>Ompok bimaculatus</em>. Different nucleotide sequences in the alignment are pointed out which vary within the species as well as between the species. Interspecific variations are designated as Molecular Operational Taxonomic Units. Thus comparison of both morphological characters and Molecular Operational Taxonomic Units in the present study helps to identify the effectiveness of both the methods together giving a better insight in coevolution of sequences with altering morphology
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Hu, Gui-Lin, Kai Gao, Ji-Shen Wang, Paul D. N. Hebert, and Bao-Zhen Hua. "Molecular phylogeny and species delimitation of the genus Dicerapanorpa (Mecoptera: Panorpidae)." Zoological Journal of the Linnean Society 187, no. 4 (2019): 1173–95. http://dx.doi.org/10.1093/zoolinnean/zlz059.
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Abstract Given that species is the fundamental unit in systematic biology, rigorous species delimitation is crucial for taxonomic studies, yet routine species delimitation remains an ongoing challenge in the taxonomic practice of insects. The two-horned scorpionfly Dicerapanorpa is a small genus in Panorpidae (Mecoptera) endemic to the Qinling-Bashan and Hengduan mountains, a biodiversity hotspot. However, species of Dicerapanorpa are difficult to delineate owing to marked intraspecific variation and interspecific similarity. Here, we investigate the diversity and species boundaries of Dicerapanorpa using an integrative approach based on DNA barcoding, morphological, geometric morphometric and molecular phylogenetic analyses. This integrative analyses confirmed the 13 described species of Dicerapanorpa and revealed three new species: Dicerapanorpa lativalva sp. nov., Dicerapanorpa hualongshana sp. nov. and Dicerapanorpa minshana sp. nov. Most molecular operational taxonomic units are in congruence with morphological clusters. Possible reasons for several discordances in Dicerapanorpa are tentatively discussed.
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Fortunato, Caroline S., David B. Carlini, Evan Ewers, and Karen L. Bushaw-Newton. "Nitrifier and denitrifier molecular operational taxonomic unit compositions from sites of a freshwater estuary of Chesapeake Bay." Canadian Journal of Microbiology 55, no. 3 (2009): 333–46. http://dx.doi.org/10.1139/w08-124.
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Temporal and spatial changes in the molecular operational taxonomic unit (OTU) compositions of bacteria harboring genes for nitrification and denitrification were assessed using denaturing gradient gel electrophoresis (DGGE), clone-based DNA sequencing of selected PCR products, and analyses of ammonium and organic matter concentrations. Sediment, overlying water, and pore-water samples were taken from different vegetated sites of Jug Bay National Estuarine Research Reserve, Maryland, during spring, summer, and fall 2006. OTU richness and the diversities of nitrifiers and denitrifiers were assessed by the presence of bands on DGGE gels, both ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) were seasonally dependent. AOB OTU richness was highest in the summer when NOB richness was decreased, whereas NOB richness was highest in the spring when AOB richness was decreased. The OTU diversities of nitrifiers did not correlate with ammonium concentrations, organic matter concentrations, or the presence of vegetation. The OTU diversities of denitrifiers possessing either the nirK or nosZ genes were not seasonally dependent but were positively correlated with organic matter content (p = 0.0015, r2 = 0.27; p < 0.0001, r2 = 0.39, respectively). Additionally, the presence of vegetation significantly enhanced nosZ species richness (Wilcoxon/Kruskal–Wallis test, p < 0.008), but this trend was not seen for nirK OTU richness. Banding patterns for nirK OTUs were more similar within sites for each season compared with any of the other genes. Over all seasons, nirK OTU richness was highest and AOB and nosZ OTU richness were lowest (Wilcoxon/Kruskal–Wallis test, p < 0.0001). High levels of sequence divergence among cloned nirK PCR products indicate a broad diversity of nirK homologs in this freshwater estuary.
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Jin, Boyang Tom, Feng Xu, Raymond T. Ng, and James C. Hogg. "Mian: interactive web-based microbiome data table visualization and machine learning platform." Bioinformatics 38, no. 4 (2021): 1176–78. http://dx.doi.org/10.1093/bioinformatics/btab754.
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Abstract Summary Mian is a web application to interactively visualize, run statistical tools and train machine learning models on operational taxonomic unit (OTU) or amplicon sequence variant (ASV) datasets to identify key taxonomic groups, diversity trends or taxonomic composition shifts in the context of provided categorical or numerical sample metadata. Tools, including Fisher’s exact test, Boruta feature selection, alpha and beta diversity, and random forest and deep neural network classifiers, facilitate open-ended data exploration and hypothesis generation on microbial datasets. Availability Mian is freely available at: miandata.org. Mian is an open-source platform licensed under the MIT license with source code available at github.com/tbj128/mian. Supplementary information Supplementary data are available at Bioinformatics online.
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Clare, Elizabeth L., Frédéric J. J. Chain, Joanne E. Littlefair, and Melania E. Cristescu. "The effects of parameter choice on defining molecular operational taxonomic units and resulting ecological analyses of metabarcoding data." Genome 59, no. 11 (2016): 981–90. http://dx.doi.org/10.1139/gen-2015-0184.
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The combination of DNA barcoding and high-throughput (next-generation) sequencing (metabarcoding) provides many promises but also serious challenges. Generating a reliable comparable estimate of biodiversity remains a central challenge to the application of the technology. Many approaches have been used to turn millions of sequences into distinct taxonomic units. However, the extent to which these methods impact the outcome of simple ecological analyses is not well understood. Here we performed a simple analysis of dietary overlap by skinks and shrews on Ile Aux Aigrettes, Mauritius. We used a combination of filtering thresholds and clustering algorithms on a COI metabarcoding dataset and demonstrate that all bioinformatics parameters will have interacting effects on molecular operational taxonomic unit (MOTU) recovery rates. These effects generated estimates covering two orders of magnitude. However, the effect on a simple ecological analysis was not large and, despite the wide variation in estimates of niche overlap, the same ecological conclusion was drawn in most cases. We advise that a conservative clustering programme coupled with larger sequence divergences to define a cluster, the removal of singletons, rigorous length filtering, and stringent match criteria for Molecular Identifier tags are preferable to avoid MOTU inflation and that the same parameters be used in all comparative analyses.
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SEMENCHENKO, ALEXANDER A., and EUGENYI A. MAKARCHENKO. "On the taxonomy and distribution of Diamesa gregsoni Edwards, (Diptera: Chironomidae: Diamesinae), with morphological redescription and DNA barcoding of species from the Far East." Zootaxa 5636, no. 3 (2025): 499–510. https://doi.org/10.11646/zootaxa.5636.3.5.
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By analyzing the DNA barcoding data of the Diamesa gregsoni Edwards syntype, we carried out a genetic study of this species from the Far East and made a comparison with DNA barcodes of North American populations. A morphological redescription of the adult male and a description of the pupa and larva are given, and the taxonomy and distribution of the species are clarified in this study. The Bayesian tree revealed two well-supported clades of D. gregsoni from Nearctic and Palaearctic. The average K2P genetic divergence between these clades was 1.67%, which corresponds to intraspecific differences. Overall intraspecific p-distances within 23 DNA barcodes of D. gregsoni were 1.19%. The Automatic Barcode Gap Discovery (ABGD), Assemble Species by Automatic Partitioning (ASAP), and Multi-rate Poisson tree processes (mPTP) approaches for the species delimitation confirmed that Nearctic and Palaearctic DNA barcodes belong to a single molecular taxonomic unit, while general mixed Yule-coalescent (GMYC) delimit the dataset into three different molecular operational taxonomic units (mOTU).
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ABEYSEKARA, SHASHIKA, HELANI SAMARASINGHE, KELUM MANAMENDRA-ARACHCHI, et al. "Taxonomic status of Pseudophilautus conniffae (Anura: Rhacophoridae) an endemic shrub frog restricted to South–Western wet zone of Sri Lanka." Zootaxa 5258, no. 1 (2023): 130–40. http://dx.doi.org/10.11646/zootaxa.5258.1.6.
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Pseudophilautus conniffae from Lowland wet zone of Sri Lanka, was described as a new species in 2019. The validity of the new species was questionable and was often challenged as it shares strong morphological resemblance with P. limbus. Moreover, the phylogenetic placement of P. conniffae was unknown as no molecular data was available until now. Here, we generated 16S DNA sequences and re-examined the external morphological characters to assess its taxonomic distinctiveness. Pseudophilautus conniffae was recovered as being close to P. limbus with strong posterior probability and bootstrap support. The uncorrected pairwise genetic distance between P. conniffae and P. limbus was negligible, being less than 0.3% for the 16S gene fragment. Further two molecular species delimitation methods, ABGD and mPTP suggested that P. conniffae and P. limbus are a single operational taxonomic unit. The Principal Component Analysis of the morphometric characters also resulted in overlapping clusters. These results suggest that the newly described P. conniffae is not a valid species and we conclude that P. conniffae as a junior synonym of P. limbus.
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Godon, Jean-Jacques, Emmanuelle Zumstein, Patrick Dabert, Frédéric Habouzit, and René Moletta. "Microbial 16S rDNA diversity in an anaerobic digester." Water Science and Technology 36, no. 6-7 (1997): 49–55. http://dx.doi.org/10.2166/wst.1997.0574.
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The bacterial community structure of a fluidized bed reactor fed by vinasses was analysed by molecular identification. After PCR amplification, three 16S rDNA clone libraries of Bacteria, Archaea, and Procarya populations were established. Community structure was determined by phylogenetic analysis of 556 partial rDNA sequences (about 500 bp long). 139 OTUs (Operational Taxonomic Unit) were found among which 133 and 6 were from the Bacteria and Archaea domains respectively. The majority of bacterial OTUs are not closely related to all other hitherto-determined sequences. The ratio Archaea/Bacteria is 1/4 and the most frequent bacterial OTU represents less than 5% of the characterised bacterial population.
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Case, Rebecca J., Yan Boucher, Ingela Dahllöf, Carola Holmström, W. Ford Doolittle, and Staffan Kjelleberg. "Use of 16S rRNA and rpoB Genes as Molecular Markers for Microbial Ecology Studies." Applied and Environmental Microbiology 73, no. 1 (2006): 278–88. http://dx.doi.org/10.1128/aem.01177-06.
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ABSTRACT Several characteristics of the 16S rRNA gene, such as its essential function, ubiquity, and evolutionary properties, have allowed it to become the most commonly used molecular marker in microbial ecology. However, one fact that has been overlooked is that multiple copies of this gene are often present in a given bacterium. These intragenomic copies can differ in sequence, leading to identification of multiple ribotypes for a single organism. To evaluate the impact of such intragenomic heterogeneity on the performance of the 16S rRNA gene as a molecular marker, we compared its phylogenetic and evolutionary characteristics to those of the single-copy gene rpoB. Full-length gene sequences and gene fragments commonly used for denaturing gradient gel electrophoresis were compared at various taxonomic levels. Heterogeneity found between intragenomic 16S rRNA gene copies was concentrated in specific regions of rRNA secondary structure. Such “heterogeneity hot spots” occurred within all gene fragments commonly used in molecular microbial ecology. This intragenomic heterogeneity influenced 16S rRNA gene tree topology, phylogenetic resolution, and operational taxonomic unit estimates at the species level or below. rpoB provided comparable phylogenetic resolution to that of the 16S rRNA gene at all taxonomic levels, except between closely related organisms (species and subspecies levels), for which it provided better resolution. This is particularly relevant in the context of a growing number of studies focusing on subspecies diversity, in which single-copy protein-encoding genes such as rpoB could complement the information provided by the 16S rRNA gene.
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Eagalle, Thanushi, and M. Alex Smith. "Diversity of parasitoid and parasitic wasps across a latitudinal gradient: Using public DNA records to work within a taxonomic impediment." FACETS 2, no. 2 (2017): 937–54. http://dx.doi.org/10.1139/facets-2016-0061.
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The diversity of insect parasitoids (Hymenoptera) has long been thought to be anomalous because it doesn’t appear to increase rapidly with decreasing latitude. However, due to the presence of undiscovered cryptic species and the under-sampling of hyper-diverse tropical areas, such apparently anomalous gradients may, in fact, be artifacts of limited geographic and taxonomic sampling. We attempted to circumvent such taxonomic impediments by elucidating a diversity/latitude relationship for parasitoid wasps, using publicly available DNA sequences to quantify diversity (via a species proxy molecular operational taxonomic unit (the DNA Barcode Index Number) and phylogenetic diversity) across a latitudinal gradient of ∼5000 km. We compared these diversity values to the abiotic factors (temperature and precipitation) that may drive the diversity/latitude relationship. We found no significant relationship between either diversity measure with latitude or with the environmental variables. Although ours is the first work to enumerate different DNA-based measures of parasitoid diversity across this geographic scale in a standardized fashion using publicly available sequences, further standardized collections over long time periods and a rapid movement of sequences into the public arena are needed to facilitate the further testing of macroecological trends elucidated with public DNA sequence libraries.
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Denys, Gaël P. J. "A comment on “Morphologic and genetic characterization of Corsican and Sardinian trout with comments on Salmo taxonomy” by Delling et al. (2020): protected Tyrrhenian trouts must be named." Knowledge & Management of Aquatic Ecosystems, no. 422 (2021): 6. http://dx.doi.org/10.1051/kmae/2021006.
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The introduction of the use of molecular data has caused debates on the taxonomy of Corsican and Sardinian trouts, also referred to as Tyrrhenian trouts (i.e. Salmo trutta, Salmo macrostigma, Salmo cettii). A recent study by Delling et al. (2020) (Morphologic and genetic characterization of Corsican and Sardinian trout with comments on Salmo taxonomy. Knowl Manage Aquat Ecosyst 421: 21) introduces important evidence regarding the taxonomy of these populations. However, their subsequent denomination as Salmo sp., that is, an undefined taxon, could have serious consequences on their future conservation management plans. Considering their threatened status, the Tyrrhenian trouts should be referred to as Salmo trutta until the ongoing taxonomic uncertainty can be unambiguously resolved. These populations must then be treated as an Evolutionary Significant Unit (ESU) or as an Operational Conservation Unit (OCU) for further conservation managements plans, as already done for other Mediterranean trout lineages.
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Arcoverde, Danilo Leal, Renata Emin-Lima, Alexandra Fernandes Costa, et al. "Evaluation of periotic–timpanic bone complex of Sotalia guianensis (Cetacea: Delphinidae) as tool in identification of geographic variations." Journal of the Marine Biological Association of the United Kingdom 94, no. 6 (2013): 1127–32. http://dx.doi.org/10.1017/s0025315413001689.
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Morphometric characteristics of the periotic–timpanic bone complex in the middle ear of cetaceans, are effective characteristics in evaluating systematics. However, they have not been used for studies of geographic variation regarding dolphins of the genus Sotalia. This study aimed to compare the periotic–timpanic of Sotalia guianensis from four distinct locations, considered here as different operational taxonomic units, Amapá/Pará (AM/PA), Maranhão/Piauí (MA/PI), Ceará (CE), and Rio de Janeiro (RJ), using 21 morphometric measurements. Multivariate analysis showed significant distinction mainly between the units of northern (AM/PA and MA/PI) and south-eastern (RJ) Brazilian coast. The timpanic bone showed variation, reaching larger sizes in the Brazilian south coast unit, corroborating current molecular data on the geographic variation of S. guianensis.
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Fortuner, Renaud, Pierre-Yves Louis, and Dominique Geniet. "On the morphometric identity of populations of Helicotylenchus pseudorobustus (Steiner, 1914) Golden, 1956 (Tylenchida: Hoplolaimidae)." Nematology 20, no. 5 (2018): 423–39. http://dx.doi.org/10.1163/15685411-00003148.
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Summary Helicotylenchus microlobus is considered to be a junior synonym of H. pseudorobustus by several authors while others consider it as valid. To clarify the status of both species, 39 samples collected from various countries were subjected to statistical analyses that showed they could be grouped into six groups. Topotypes of H. pseudorobustus and H. microlobus belong to two different groups. However, samples in the other groups were morphologically intermediate between these two groups. Characters used in the past to uphold the validity of H. microlobus were variable and overlapping from group to group. The 28 samples studied are identified as H. pseudorobustus. Helicotylenchus microlobus, H. bradys and H. phalerus are confirmed as junior synonyms of H. pseudorobustus. There was no complete congruence between the morphological groups and molecular groups proposed by other authors. For these, two MOTU (Molecular Operational Taxonomic Unit) are accepted within H. pseudorobustus.
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Loginov, S. N., A. S. Batomunkuev, A. A. Sukhinin, et al. "Molecular biological characteristics of the intestinal microbiocenosis of dogs on a mixed diet." International Journal of Veterinary Medicine, no. 4 (January 16, 2025): 59–71. https://doi.org/10.52419/issn2072-2419.2024.4.59.
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Metabarcoding research of the domestic animal intestines is relevant for veterinary medicine. The effect of feeding and food additives on its gut microbiome is of both applied and fundamental significance and demonstrates the stimulation of the various groups of bacteria development. The objective of our work is to study the effect of the domestic complete pet feed Dilly on the microbial community of the dogs’ intestines in breeding kennel of Irkutsk. The microbiome composition was determined in 12 animals of different ages having used Illumina MiSeq amplicon sequencing of the V3-V4 region of 16S rRNA. Rates diversity had been adapted to evaluate the affluence and prominence of Bacterial operational and taxonomic units and nonparametric Mann-Whitney criteria (correlative test, p≤0,05) used to evaluate the certainty value of the difference of operational and taxonomic unit percentage in different physiological groups. All in all, 147150 the 16S rRNA gene fragment sequences were obtained. The dominant bacteria turned out to be the phyla Firmicutes, Actinobacteriota, Bacteroidota, and Proteobacteria. The animals that had been under research had almost no Fusobacteriota bacteria - markers of a diet with a predominance of raw meat (predation). The Firmicutes phylum included bacteria from five families. The most numerous families among the Firmicutes were the Lactobacillaceae bacteria. Representatives of seven families were observed among Actinobacteriota bacteria, of which Bifidobacteriaceae predominated. Proteobacteria of the Enterobacterales order and Burkholderiales made up a small proportion of the entire community and depended on the animal age. The research result could be used in perspective to enlarge knowledge about the digestive process in an omnivorous animal of the wolf pack. These animals have a more or less flexible microbiome, which has several variants of normal composition. There predominated lactic acid bacteria in the microbial communities of the dogs’ intestines, which consumed feed that contained coarse dietary fibers. In its turn, lactic acid bacteria reduced the number of Fusobacteriota.
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Lan, Chuan-Ching, and Donald R. Love. "Molecular Characterisation of Bacterial Community Structure along the Intestinal Tract of Zebrafish (Danio rerio): A Pilot Study." ISRN Microbiology 2012 (February 14, 2012): 1–10. http://dx.doi.org/10.5402/2012/590385.
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The bacterial composition along the intestinal tract of Danio rerio was investigated by cultivation-independent analysis of the 16S rRNA gene. Clone libraries were constructed for three compartments of the intestinal tract of individual fish. 566 individual clones were differentiated by amplified 16S rRNA gene restriction analysis (ARDRA), and clone representatives from each operational taxonomic unit (OTU) were sequenced. As reported in other studies, we found that Proteobacteria was the most prominent phylum among clone libraries from different fish. Data generated from this pilot study indicated some compositional differences in bacterial communities. Two dominant classes, Gammaproteobacteria and Bacilli, displayed different levels of abundance in different compartments; Gammaproteobacteria increased along the intestinal tract, while Bacilli decreased its abundance along the proximal-distal axis. Less obvious spatial patterns were observed for other classes. In general, bacterial diversity in the intestinal bulb was greater than that in the posterior intestine. Interindividual differences in bacterial diversity and composition were also noted in this study.
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Öpik, Maarja, John Davison, Mari Moora, and Martin Zobel. "DNA-based detection and identification of Glomeromycota: the virtual taxonomy of environmental sequences." Botany 92, no. 2 (2014): 135–47. http://dx.doi.org/10.1139/cjb-2013-0110.
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An increasing number of case studies are reporting Glomeromycota molecular diversity from ecosystems worldwide. Typically, phylogroups that can be related to morphospecies and those that remain unidentified (“environmental”) are recorded. To compare such data and generalise observed patterns, the principles underlying sequence identification should be unified. Data from case studies are collected and systematized in a public database MaarjAM ( http://www.maarjam.botany.ut.ee ), which applies a unique molecular operational taxonomic unit (MOTU) nomenclature: virtual taxa (VT) are phylogenetically defined sequence groups roughly corresponding to species-level taxa. VT are based on type sequences, making them consistent in time, but they also evolve: they can be split or merged, when necessary. This system allows standardisation of original MOTU designations and, much like binomial taxonomic nomenclature, comparison and consistency between studies. Refinement of VT delimitation principles and comparability with traditional Glomeromycota taxonomy will benefit from more information about intra- vs. inter-specific nucleotide variation in Glomeromycota, sequencing of morphospecies, and resolution of issues in Glomeromycota taxonomy. As the recorded number of VT already exceeds the number of Glomeromycota morphospecies, designation of species based on DNA alone appears a necessity in the near future. Application of VT is becoming widespread, and MaarjAM database is increasingly used as a reference for environmental sequence identification. The current status and future prospects of arbuscular mycorrhizal fungi (AMF) DNA-based identification and community description are presented.
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Smith, M. Alex, Brian L. Fisher, and Paul D. N. Hebert. "DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar." Philosophical Transactions of the Royal Society B: Biological Sciences 360, no. 1462 (2005): 1825–34. http://dx.doi.org/10.1098/rstb.2005.1714.
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The role of DNA barcoding as a tool to accelerate the inventory and analysis of diversity for hyperdiverse arthropods is tested using ants in Madagascar. We demonstrate how DNA barcoding helps address the failure of current inventory methods to rapidly respond to pressing biodiversity needs, specifically in the assessment of richness and turnover across landscapes with hyperdiverse taxa. In a comparison of inventories at four localities in northern Madagascar, patterns of richness were not significantly different when richness was determined using morphological taxonomy (morphospecies) or sequence divergence thresholds (Molecular Operational Taxonomic Unit(s); MOTU). However, sequence-based methods tended to yield greater richness and significantly lower indices of similarity than morphological taxonomy. MOTU determined using our molecular technique were a remarkably local phenomenon—indicative of highly restricted dispersal and/or long-term isolation. In cases where molecular and morphological methods differed in their assignment of individuals to categories, the morphological estimate was always more conservative than the molecular estimate. In those cases where morphospecies descriptions collapsed distinct molecular groups, sequence divergences of 16% (on average) were contained within the same morphospecies. Such high divergences highlight taxa for further detailed genetic, morphological, life history, and behavioral studies.
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Echart-Almeida, Cinara, and Suzana Cavalli-Molina. "Hordein variation in Brazilian barley varieties (Hordeum vulgare L.) and wild barley (H. euclaston Steud. and H. stenostachys Godr.)." Genetics and Molecular Biology 23, no. 2 (2000): 425–33. http://dx.doi.org/10.1590/s1415-47572000000200031.
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SDS-PAGE was used to analyze the hordein polypeptide patterns of Brazilian barley varieties (Hordeum vulgare L.) and of two native species of Hordeum from southern Brazil (H. euclaston Steud. and H. stenostachys Godr.). Forty different hordein polypeptide bands with molecular weights ranging from 30 to 94 kDa were found in the seeds of the three species studied. Twelve of the 14 varieties examined showed intravarietal polymorphism. The number of bands ranged from 10 to 17, depending on the variety, and from 3 to 13 among individual seeds, with a total of 26 bands in H. vulgare. Phenograms using each seed as an operational taxonomic unit (OTU) showed that the seeds from most varieties did not form distinct clusters. Seeds from different plants of the native species varied considerably. The molecular weights of the hordein polypeptides of the two native species were quite different from those of H. vulgare. There was a greater similarity between the native species than with H. vulgare, although H. stenostachys was slightly closer to the cultivated species than H. euclaston.
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Yang, Guangju, Wenjing Wang, Yuwei Tong, and Zhijun Zhou. "Species delimitation and DNA barcoding for Chinese Mantodea (Insecta, Dictyoptera)." ZooKeys 1229 (February 24, 2025): 25–42. https://doi.org/10.3897/zookeys.1229.129123.
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DNA barcoding has been proposed as a rapid and reliable tool for animal identification and species delineation. The 5’ end of the mitochondrial cytochrome c oxidase I gene (COI-5P) was sequenced for 318 specimens of 55 mantis species. Of these, 44 species had not been sequenced before, thus being new COI-5P barcode sequences to science. Another 61 COI-5P barcode sequences comprising five species were retrieved from the Barcode of Life Database (BOLD; www.boldsystems.org). Five species delimitation algorithms were employed to sort barcode sequences into Molecular Operational Taxonomic Units (MOTUs), namely the distance-based Barcode Index Number (BIN) System, Generalized Mixed Yule Coalescent (GMYC), a Java program that uses an explicit, determinate algorithm to define Molecular Operational Taxonomic Unit (jMOTU), Assemble Species by Automatic Partitioning (ASAP), and Bayesian implementation of the Poisson Tree Processes model (bPTP). All species, except Hierodula chinensis Werner, 1929, were recovered as monophyletic on the neighbor-joining (NJ) tree. For the final dataset, 379 COI-5P barcode sequences were assigned to 68 BINs. Fifty-five out of 68 BINs obtained were new to BOLD. The low level of BIN overlap with other nations highlights the importance of constructing a regional DNA barcode reference library. The algorithms ASAP, jMOTU, bPTP, and GMYC clustered barcode sequences into 32, 58, 68, and 60 MOTUs, respectively. All species delimitation algorithms (except ASAP analysis) split Anaxarcha sinensis Beier, 1933, Anaxarcha zhengi Ren & Wang, 1994, H. chinensis, Spilomantis occipitalis (Westwood, 1889), Titanodula formosana Giglio-Tos, 1912 into more than one MOTUs. All algorithms merged Hierodula sp. BCM-2019 and H. chinensis into the same MOTU, as for Tenodera aridifolia Stoll, 1813 and Tenodera sinensis Saussure, 1871. More accurate identification results need to be supplemented by detailed morphological classification.
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Yang, Guangju, Wenjing Wang, Yuwei Tong, and Zhijun Zhou. "Species delimitation and DNA barcoding for Chinese Mantodea (Insecta, Dictyoptera)." ZooKeys 1229 (February 24, 2025): 25–42. https://doi.org/10.3897/zookeys.1229.129123.
Full textAbstract:
DNA barcoding has been proposed as a rapid and reliable tool for animal identification and species delineation. The 5' end of the mitochondrial cytochrome <i>c</i> oxidase I gene (COI-5P) was sequenced for 318 specimens of 55 mantis species. Of these, 44 species had not been sequenced before, thus being new COI-5P barcode sequences to science. Another 61 COI-5P barcode sequences comprising five species were retrieved from the Barcode of Life Database (BOLD; www.boldsystems.org). Five species delimitation algorithms were employed to sort barcode sequences into Molecular Operational Taxonomic Units (MOTUs), namely the distance-based Barcode Index Number (BIN) System, Generalized Mixed Yule Coalescent (GMYC), a Java program that uses an explicit, determinate algorithm to define Molecular Operational Taxonomic Unit (jMOTU), Assemble Species by Automatic Partitioning (ASAP), and Bayesian implementation of the Poisson Tree Processes model (bPTP). All species, except <i>Hierodula chinensis</i> Werner, 1929, were recovered as monophyletic on the neighbor-joining (NJ) tree. For the final dataset, 379 COI-5P barcode sequences were assigned to 68 BINs. Fifty-five out of 68 BINs obtained were new to BOLD. The low level of BIN overlap with other nations highlights the importance of constructing a regional DNA barcode reference library. The algorithms ASAP, jMOTU, bPTP, and GMYC clustered barcode sequences into 32, 58, 68, and 60 MOTUs, respectively. All species delimitation algorithms (except ASAP analysis) split <i>Anaxarcha sinensis</i> Beier, 1933, <i>Anaxarcha zhengi</i> Ren & Wang, 1994, <i>H. chinensis</i>, <i>Spilomantis occipitalis</i> (Westwood, 1889), <i>Titanodula formosana</i> Giglio-Tos, 1912 into more than one MOTUs. All algorithms merged <i>Hierodula</i> sp. BCM-2019 and <i>H. chinensis</i> into the same MOTU, as for <i>Tenodera aridifolia</i> Stoll, 1813 and <i>Tenodera sinensis</i> Saussure, 1871. More accurate identification results need to be supplemented by detailed morphological classification.
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Taylor, Peter J., Angus Macdonald, Steven M. Goodman, et al. "Integrative taxonomy resolves three new cryptic species of small southern African horseshoe bats (Rhinolophus)." Zoological Journal of the Linnean Society 184, no. 4 (2018): 1249–76. http://dx.doi.org/10.1093/zoolinnean/zly024.
Full textAbstract:
Abstract Examination of historical and recent collections of small Rhinolophus bats revealed cryptic taxonomic diversity within southern African populations previously referred to as R. swinnyi Gough, 1908 and R. landeri Martin, 1832. Specimens from Mozambique morphologically referable to R. swinnyi were phylogenetically unrelated to topotypic R. swinnyi from the Eastern Cape Province of South Africa based on cytochrome b sequences and showed distinctive echolocation, baculum and noseleaf characters. Due to their genetic similarity to a previously reported molecular operational taxonomic unit (OTU) from north-eastern South Africa, Zimbabwe and Zambia, we recognize the available synonym (R. rhodesiae Roberts, 1946) to denote this distinct evolutionary species. This new taxon is genetically identical to R. simulator K. Andersen, 1904 based on mtDNA and nuclear DNA sequences but can easily be distinguished on morphological and acoustic grounds. We attribute this genetic similarity to historical introgression, a frequently documented phenomenon in bats. An additional genetically distinct and diminutive taxon in the swinnyi s.l. group (named herein, R. gorongosae sp. nov.) is described from Gorongosa National Park, central Mozambique. Specimens from Mozambique referable based on morphology to R. landeri were distinct from topotypic landeri from West Africa based on mtDNA sequences, and acoustic, noseleaf and baculum characters. This Mozambique population is assigned to the available synonym R. lobatus Peters, 1952.
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Kaltenbach, Thomas, Jhoana M. Garces, and Jean-Luc Gattolliat. "The success story of Labiobaetis Novikova & Kluge in the Philippines (Ephemeroptera, Baetidae), with description of 18 new species." ZooKeys 1002 (December 10, 2020): 1–114. https://doi.org/10.3897/zookeys.1002.58017.
Full textAbstract:
Material collected between 1994 and 2020 in the Philippines, covering most main islands like Luzon, Mindoro, Palawan, Negros, Cebu, Leyte, and Mindanao and some smaller islands, substantially increased our knowledge of Labiobaetis Novikova & Kluge in this archipelago. Only three species were previously reported: L. molawinensis (Müller-Liebenau, 1982) and L. sumigarensis (Müller-Liebenau, 1982) from larvae and L. boettgeri (Ulmer, 1924) from adults. Eighteen new species have been identified using a combination of morphology and genetic distance (COI, Kimura 2-parameter). They are described and illustrated based on their larvae and a key to all species in the Philippines is provided. The total number of Labiobaetis in the Philippines has increased to 21 species. Additional diversity of Labiobaetis based on molecular evidence only is presented as Molecular Operational Taxonomic Units (MOTUs) without description. The interspecific K2P distances in the Philippines are between 15% and 27%, the intraspecific distances are usually between 0% and 3%. The total number of Labiobaetis species worldwide is augmented to 144.
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WIJAYATHILAKA, NAYANA, USHANI PERERA, KELUM MANAMENDRA-ARACHCHI, et al. "Pseudophilautus pardus, a junior synonym of P. viridis (Amphibia: Anura: Rhacophoridae)." Zootaxa 5227, no. 4 (2023): 459–72. http://dx.doi.org/10.11646/zootaxa.5227.4.4.
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Pseudophilautus pardus, was first described in 2007, based on a single specimen collected in Sri Lanka during the 19th century. Its absence in recent surveys suggested that the species was extinct. The distinctive spotted dorsal coloration, together with other morphological features, was used to distinguish it from congeners. In 2013, we discovered a specimen resembling the holotype of P. pardus in Samanala Strict Nature Reserve. A DNA analysis based on the 16S rRNA mt-DNA locus recovered a low uncorrected pairwise genetic distance of 0.77–0.96% between the recent example of ‘P. pardus’ and a congener, P. viridis. Molecular species delimitation methods suggest P. pardus and P. virids to be a single operational taxonomic unit. Morphological analyses using the freshly collected specimen, together with numerous photographic records show P. viridis to be a highly polychromatic species within which the coloration observed in P. pardus too occurs, though rarely. We conclude that P. pardus is a junior synonym of P. viridis.
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Taylor, Peter J., Angus Macdonald, Steven M. Goodman, et al. "Integrative taxonomy resolves three new cryptic species of small southern African horseshoe bats (Rhinolophus)." Zoological Journal of the Linnean Society 184, no. 4 (2018): 1249–76. https://doi.org/10.5281/zenodo.13417268.
Full textAbstract:
(Uploaded by Plazi for the Bat Literature Project) Abstract Examination of historical and recent collections of small Rhinolophus bats revealed cryptic taxonomic diversity within southern African populations previously referred to as R. swinnyi Gough, 1908 and R. landeri Martin, 1832. Specimens from Mozambique morphologically referable to R. swinnyi were phylogenetically unrelated to topotypic R. swinnyi from the Eastern Cape Province of South Africa based on cytochrome b sequences and showed distinctive echolocation, baculum and noseleaf characters. Due to their genetic similarity to a previously reported molecular operational taxonomic unit (OTU) from north-eastern South Africa, Zimbabwe and Zambia, we recognize the available synonym (R. rhodesiae Roberts, 1946) to denote this distinct evolutionary species. This new taxon is genetically identical to R. simulator K. Andersen, 1904 based on mtDNA and nuclear DNA sequences but can easily be distinguished on morphological and acoustic grounds. We attribute this genetic similarity to historical introgression, a frequently documented phenomenon in bats. An additional genetically distinct and diminutive taxon in the swinnyi s.l. group (named herein, R. gorongosae sp. nov.) is described from Gorongosa National Park, central Mozambique. Specimens from Mozambique referable based on morphology to R. landeri were distinct from topotypic landeri from West Africa based on mtDNA sequences, and acoustic, noseleaf and baculum characters. This Mozambique population is assigned to the available synonym R. lobatus Peters, 1952.
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Taylor, Peter J., Angus Macdonald, Steven M. Goodman, et al. "Integrative taxonomy resolves three new cryptic species of small southern African horseshoe bats (Rhinolophus)." Zoological Journal of the Linnean Society 184, no. 4 (2018): 1249–76. https://doi.org/10.5281/zenodo.13417268.
Full textAbstract:
(Uploaded by Plazi for the Bat Literature Project) Abstract Examination of historical and recent collections of small Rhinolophus bats revealed cryptic taxonomic diversity within southern African populations previously referred to as R. swinnyi Gough, 1908 and R. landeri Martin, 1832. Specimens from Mozambique morphologically referable to R. swinnyi were phylogenetically unrelated to topotypic R. swinnyi from the Eastern Cape Province of South Africa based on cytochrome b sequences and showed distinctive echolocation, baculum and noseleaf characters. Due to their genetic similarity to a previously reported molecular operational taxonomic unit (OTU) from north-eastern South Africa, Zimbabwe and Zambia, we recognize the available synonym (R. rhodesiae Roberts, 1946) to denote this distinct evolutionary species. This new taxon is genetically identical to R. simulator K. Andersen, 1904 based on mtDNA and nuclear DNA sequences but can easily be distinguished on morphological and acoustic grounds. We attribute this genetic similarity to historical introgression, a frequently documented phenomenon in bats. An additional genetically distinct and diminutive taxon in the swinnyi s.l. group (named herein, R. gorongosae sp. nov.) is described from Gorongosa National Park, central Mozambique. Specimens from Mozambique referable based on morphology to R. landeri were distinct from topotypic landeri from West Africa based on mtDNA sequences, and acoustic, noseleaf and baculum characters. This Mozambique population is assigned to the available synonym R. lobatus Peters, 1952.
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Taylor, Peter J., Angus Macdonald, Steven M. Goodman, et al. "Integrative taxonomy resolves three new cryptic species of small southern African horseshoe bats (Rhinolophus)." Zoological Journal of the Linnean Society 184, no. 4 (2018): 1249–76. https://doi.org/10.5281/zenodo.13417268.
Full textAbstract:
(Uploaded by Plazi for the Bat Literature Project) Abstract Examination of historical and recent collections of small Rhinolophus bats revealed cryptic taxonomic diversity within southern African populations previously referred to as R. swinnyi Gough, 1908 and R. landeri Martin, 1832. Specimens from Mozambique morphologically referable to R. swinnyi were phylogenetically unrelated to topotypic R. swinnyi from the Eastern Cape Province of South Africa based on cytochrome b sequences and showed distinctive echolocation, baculum and noseleaf characters. Due to their genetic similarity to a previously reported molecular operational taxonomic unit (OTU) from north-eastern South Africa, Zimbabwe and Zambia, we recognize the available synonym (R. rhodesiae Roberts, 1946) to denote this distinct evolutionary species. This new taxon is genetically identical to R. simulator K. Andersen, 1904 based on mtDNA and nuclear DNA sequences but can easily be distinguished on morphological and acoustic grounds. We attribute this genetic similarity to historical introgression, a frequently documented phenomenon in bats. An additional genetically distinct and diminutive taxon in the swinnyi s.l. group (named herein, R. gorongosae sp. nov.) is described from Gorongosa National Park, central Mozambique. Specimens from Mozambique referable based on morphology to R. landeri were distinct from topotypic landeri from West Africa based on mtDNA sequences, and acoustic, noseleaf and baculum characters. This Mozambique population is assigned to the available synonym R. lobatus Peters, 1952.
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Barnes, Christopher J., Linett Rasmussen, Maria Asplund, et al. "Comparing DADA2 and OTU clustering approaches in studying the bacterial communities of atopic dermatitis." Journal of Medical Microbiology 69, no. 11 (2020): 1293–302. http://dx.doi.org/10.1099/jmm.0.001256.
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Introduction. The pathogenesis of atopic dermatitis (AD) is not yet fully understood, but the bacterial composition of AD patients’ skin has been shown to have an increased abundance of Staphylococcus aureus . More recently, coagulase-negative Staphylococcus (CoNS) species were shown to be able to inhibit S. aureus , but further studies are required to determine the effects of Staphylococcus community variation in AD. Aim. Here we investigated whether analysing metabarcoding data with the more recently developed DADA2 approach improves metabarcoding analyses compared to the previously used operational taxonomic unit (OTU) clustering, and can be used to study Staphylococcus community dynamics. Methods. The bacterial 16S rRNA region from tape strip samples of the stratum corneum of AD patients (non-lesional skin) and non-AD controls was metabarcoded. We processed metabarcoding data with two different bioinformatic pipelines (an OTU clustering method and DADA2), which were analysed with and without technical replication (sampling strategy). Results. We found that OTU clustering and DADA2 performed well for community-level studies, as demonstrated by the identification of significant differences in the skin bacterial communities associated with AD. However, the OTU clustering approach inflated bacterial richness, which was worsened by not having technical replication. Data processed with DADA2 likely handled sequencing errors more effectively and thereby did not inflate molecular richness. Conclusion. We believe that DADA2 represents an improvement over an OTU clustering approach, and that biological replication rather than technical replication is a more effective use of resources. However, neither OTU clustering nor DADA2 gave insights into Staphylococcus community dynamics, and caution should remain in not overinterpreting the taxonomic assignments at lower taxonomic ranks.
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Muhammad, Buhari Lawan, Taehee Kim, and Jang-Seu Ki. "18S rRNA Analysis Reveals High Diversity of Phytoplankton with Emphasis on a Naked Dinoflagellate Gymnodinium sp. at the Han River (Korea)." Diversity 13, no. 2 (2021): 73. http://dx.doi.org/10.3390/d13020073.
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Biomonitoring of phytoplankton communities in freshwater ecosystems is imperative for efficient water quality management. In the present study, we present the seasonal diversity of phytoplankton from the non-reservoir area of the Han River (Korea), assessed using the 18S rRNA amplicon sequencing. Our results uncovered a considerably high eukaryotic diversity, which was predominantly represented by phytoplankton in all the seasons (38–63%). Of these, the diatoms, Cyclostephanos tholiformis, Stephanodiscus hantzschii, and Stephanodiscus sp., were frequently detected in spring and winter. Interestingly, for the first time in the Han River, we detected a large number of operational taxonomic unit (OTU) reads belonging to the naked dinoflagellate Gymnodinium sp., which dominated in autumn (15.8%) and was observed only in that season. Molecular cloning and quantitative real-time polymerase chain reaction (PCR) confirmed the presence of Gymnodinium sp. in the samples collected in 2012 and 2019. Moreover, a comparison of the present data with our previous data from a reservoir area (Paldang Dam) revealed similar patterns of phytoplankton communities. This molecular approach revealed a prospective toxic species that was not detected through microscopy. Collectively, resolving phytoplankton communities at a level relevant for water quality management will provide a valuable reference for future studies on phytoplankton for environmental monitoring.
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Ringel-Kulka, Tamar, Andrew K. Benson, Ian M. Carroll, Jaehyoung Kim, Ryan M. Legge, and Yehuda Ringel. "Molecular characterization of the intestinal microbiota in patients with and without abdominal bloating." American Journal of Physiology-Gastrointestinal and Liver Physiology 310, no. 6 (2016): G417—G426. http://dx.doi.org/10.1152/ajpgi.00044.2015.
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Recent studies have demonstrated differences in the intestinal microbiota between patients with irritable bowel syndrome (IBS) and healthy controls (HC), suggesting a role for the intestinal microbiota in the pathogenesis of IBS. Alterations in the microbiota have also been implicated in the pathogenesis of abdominal bloating, a commonly reported symptom in IBS. We investigated the relationship between the intestinal microbiota, abdominal bloating, and altered bowel patterns in a cohort of patients with IBS and HC. The 16S rRNA gene from fresh fecal samples was amplified and pyrosequenced by using Roche-454 Titanium chemistry. A Core Measurable Microbiome (CMM) was generated for Operational Taxonomic Unit (OTU) detected in >75% of all samples and compositional features of CMM were compared between groups by Linear Discriminant Analysis (LDA). IBS differentiated from HC by LDA using continuous variation in the species/OTUs or the CMM genera. When subcategorized based on bloating symptoms and bowel characteristics, the same subjects were also well differentiated from one another and from HC. ANOVA analysis showed quantitative species/OTU differences between the subgroups including IBS with and without bloating, and subtypes based on bowel characteristics. The clear LDA differentiation and the significant microbial taxa differences between the groups imply a significant association of the microbiota with bloating symptoms and bowel characteristics in IBS. These changes in the microbiota may serve as a biomarker for IBS and its clinical subtypes and suggest a role for the intestinal microbiota in the pathogenesis of the main symptoms of the disorder.
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Zemouri, Charifa, Alexa M. G. A. Laheij, Catherine M. C. Volgenant, et al. "Chlorine-based DUWL disinfectant leads to a different microbial composition of water derived biofilms compared to H2O2-based chemical disinfectants in vitro." PeerJ 8 (July 15, 2020): e9503. http://dx.doi.org/10.7717/peerj.9503.
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Background Biofilm formation in dental unit waterlines (DUWL) may lead to health risks for dental staff and patients. Therefore, dental unit waterlines need to be disinfected, for instance by using chemical disinfectants. However, the application of chemical disinfectants may lead to the selection of specific microorganisms. Therefore, the aim of our study was to assess the microbial composition of water-derived biofilms, after a continuous exposure to maintenance doses of commercially available chemical disinfectants, in vitro. Methods The AAA-model was used to grow water derived biofilms. The biofilms were subjected to the maintenance dose of each disinfectant. To determine the microbial composition, the V4 hypervariable region of the 16S rRNA gene was sequenced. The sequences were clustered in operational taxonomic units (OTUs). Results The bacterial composition of biofilms in all treatment groups differed significantly (PERMANOVA F = 4.441, p = 0.001). Pairwise comparisons revealed Anoxyl treated biofilms were significantly different from all groups (p = 0.0001). In the Anoxyl-treated biofilms, the relative abundance of Comamonadaceae and Sphingopyxis was high compared to the Dentosept, Green and Clean and Oxygenal groups. Conclusion We concluded that exposure to low doses of the chlorine-based chemical disinfectant Anoxyl led to a substantially different composition of water derived biofilms compared to biofilms exposed to H2O2-based chemical disinfectants.
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Wang, Jianjun, Yong Zhang, Zhengkui Li, and Ji Shen. "Higher seasonal variation of actinobacterial communities than spatial heterogeneity in the surface sediments of Taihu Lake, China." Canadian Journal of Microbiology 59, no. 5 (2013): 353–58. http://dx.doi.org/10.1139/cjm-2012-0663.
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Much more attention has been paid to the actinobacterial community in soils or water columns of aquatic habitats. However, there are few studies on their composition and diversity in lake sediments. Here, we used denaturing gradient gel electrophoresis and clone libraries of partial 16S rRNA gene to study the spatial variations of actinobacterial communities across 4 seasons in the surface sediments of the shallow, subtropical Taihu Lake. Cluster analysis based on fingerprints showed clear spatiotemporal variations of actinobacterial communities and higher seasonal variation than spatial heterogeneity. Based on clone libraries, this pattern was supported by the principal coordinates analysis in the phylogenetic context and by detrended correspondence analysis on the operational taxonomic unit table. Additionally, phylogenetic analysis showed that the putative freshwater-specific actinobacterial lineages (e.g., acI) were also detected in the lake sediments, which suggests that these subclusters may also adapt to the sediment environments. Summarily, our results suggested that actinobacterial communities of the surface sediments were more affected by seasonal variation than spatial heterogeneity in the intrahabitat of Taihu Lake.
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Huang, Rui, Dayong Zhao, Jin Zeng, et al. "pH affects bacterial community composition in soils across the Huashan Watershed, China." Canadian Journal of Microbiology 62, no. 9 (2016): 726–34. http://dx.doi.org/10.1139/cjm-2015-0783.
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To investigate soil bacterial richness and diversity and to determine the correlations between bacterial communities and soil properties, 8 soil samples were collected from the Huashan watershed in Anhui, China. Subsequently, 454 high-throughput pyrosequencing and bioinformatics analyses were performed to examine the soil bacterial community compositions. The operational taxonomic unit richness of the bacterial community ranged from 3664 to 5899, and the diversity indices, including Chao1, Shannon–Wiener, and Faith’s phylogenetic diversity ranged from 7751 to 15 204, 7.386 to 8.327, and 415.77 to 679.11, respectively. The 2 most dominant phyla in the soil samples were Actinobacteria and Proteobacteria. The richness and diversity of the bacterial community were positively correlated with soil pH. The Mantel test revealed that the soil pH was the dominant factor influencing the bacterial community. The positive modular structure of co-occurrence patterns at the genus level was discovered by network analysis. The results obtained in this study provide useful information that enhances our understanding of the effects of soil properties on the bacterial communities.
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Jamdade, Rahul, Kareem A. Mosa, Ali El-Keblawy, et al. "DNA Barcodes for Accurate Identification of Selected Medicinal Plants (Caryophyllales): Toward Barcoding Flowering Plants of the United Arab Emirates." Diversity 14, no. 4 (2022): 262. http://dx.doi.org/10.3390/d14040262.
Full textAbstract:
The need for herbal medicinal plants is steadily increasing. Hence, the accurate identification of plant material has become vital for safe usage, avoiding adulteration, and medicinal plant trading. DNA barcoding has shown to be a valuable molecular identification tool for medicinal plants, ensuring the safety and efficacy of plant materials of therapeutic significance. Using morphological characters in genera with closely related species, species delimitation is often difficult. Here, we evaluated the capability of the nuclear barcode ITS2 and plastid DNA barcodes rbcL and matK to identify 20 medicinally important plant species of Caryophyllales. In our analysis, we applied an integrative approach for species discrimination using pairwise distance-based unsupervised operational taxonomic unit “OTU picking” methods, viz., ABGD (Automated Barcode Gap Analysis) and ASAP (Assemble Species by Automatic Partitioning). Along with the unsupervised OTU picking methods, Supervised Machine Learning methods (SML) were also implemented to recognize divergent taxa. Our results indicated that ITS2 was more successful in distinguishing between examined species, implying that it could be used to detect the contamination and adulteration of these medicinally important plants. Moreover, this study suggests that the combination of more than one method could assist in the resolution of morphologically similar or closely related taxa.
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Cheon, J., F. Hong, T. Hidaka, H. Koshikawa, and H. Tsuno. "Microbial population dynamics in a thermophilic methane digester fed with garbage." Water Science and Technology 55, no. 10 (2007): 175–82. http://dx.doi.org/10.2166/wst.2007.320.
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The diversity of microbial communities in three full-scale thermophilic anaerobic digesters which treated garbage, sewage sludge and livestock wastes (hereafter called TGD, TSD and TLD, respectively) was investigated using 16S rDNA clone libraries in triplicate. The population dynamics of TGD were also studied. The purposes were to show the microbial diversity in each reactor and to suggest which key microbes in a thermophilic methane digester fed with garbage, including a check of reproducibility and the suggestion of an error range in this molecular biology method. 736 clones were identified, and the maximum error was estimated to be around ±10% for the same OTU (operational taxonomic unit) and for most detected OTUs. The most frequently detected OTU shows a close relationship to Uncultured bacterium clone MBA08,Unidentified bacterium clone TUG22 and Uncultured archaeal symbiont PA204 in TGD, TSD and TLD, respectively. The microbial population dynamics in TGD were studied over a period of 90 days, and the occupying ratios of Bacillus infernus and Methanothermobacter wolfeii were shown to change with the change in VFA concentration. From the dynamic change and characteristics of the microbes, it is concluded that Bacillus infernus and Methanothermobacter wolfeii played an important role and were recommended as key microbes in TGD.
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Joyner, Jennifer J., R. Wayne Litaker, and Hans W. Paerl. "Morphological and Genetic Evidence that the Cyanobacterium Lyngbya wollei (Farlow ex Gomont) Speziale and Dyck Encompasses at Least Two Species." Applied and Environmental Microbiology 74, no. 12 (2008): 3710–17. http://dx.doi.org/10.1128/aem.02645-07.
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ABSTRACT Dense blooms of the cyanobacterium Lyngbya wollei are increasingly responsible for declining water quality and habitat degradation in numerous springs, rivers, and reservoirs. This research represents the first molecular phylogenetic analysis of L. wollei in comparison with the traditional morphological characterization of this species. Specimens were collected from several springs in Florida and a reservoir in North Carolina. Segments of the small-subunit (SSU) rRNA and nifH genes were PCR amplified, cloned, and sequenced. The phylogenetic analysis of the SSU rRNA gene revealed sequences that fell into three distinct subclusters, each with >97% sequence similarity. These were designated operational taxonomic unit 1 (OTU1), OTU2, and OTU3. Similarly, the nifH sequences fell into three distinct subclusters named S1, S2, and S3. When either bulk samples or individual filaments were analyzed, we recovered OTU1 with S1, OTU2 with S2, and OTU3 with S3. The coherence between the three SSU rRNA gene and nifH subclusters was consistent with genetically distinct strains or species. Cells associated with subclusters OTU3 and S3 were significantly wider and longer than those associated with other subclusters. The combined molecular and morphological data indicate that the species commonly identified as L. wollei in the literature represents two or possibly more species. Springs containing OTU3 and S3 demonstrated lower ion concentrations than other collection sites. Geographical locations of Lyngbya subclusters did not correlate with residual dissolved inorganic nitrogen or phosphorus concentrations. This study emphasizes the need to complement traditional identification with molecular characterization to more definitively detect and characterize harmful cyanobacterial species or strains.
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Benucci, Gian Maria Niccolò, Reid Longley, Peng Zhang, Qi Zhao, Gregory Bonito, and Fuqiang Yu. "Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses." PeerJ 7 (September 26, 2019): e7744. http://dx.doi.org/10.7717/peerj.7744.
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Morels (Morchella spp.) are iconic edible mushrooms with a long history of human consumption. Some microbial taxa are hypothesized to be important in triggering the formation of morel primordia and development of fruiting bodies, thus, there is interest in the microbial ecology of these fungi. To identify and compare fungal and prokaryotic communities in soils where Morchella sextelata is cultivated in outdoor greenhouses, ITS and 16S rDNA high throughput amplicon sequencing and microbiome analyses were performed. Pedobacter, Pseudomonas, Stenotrophomonas, and Flavobacterium were found to comprise the core microbiome of M. sextelata ascocarps. These bacterial taxa were also abundant in the soil beneath growing fruiting bodies. A total of 29 bacterial taxa were found to be statistically associated to Morchella fruiting bodies. Bacterial community network analysis revealed high modularity with some 16S rDNA operational taxonomic unit clusters living in specialized fungal niches (e.g., pileus, stipe). Other fungi dominating the soil mycobiome beneath morels included Morchella, Phialophora, and Mortierella. This research informs understanding of microbial indicators and potential facilitators of Morchella ecology and fruiting body production.
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Berhe, Tesfemariam, Richard Ipsen, Eyassu Seifu, Mohamed Y. Kurtu, Angelina Fugl, and Egon Bech Hansen. "Metagenomic analysis of bacterial community composition in Dhanaan: Ethiopian traditional fermented camel milk." FEMS Microbiology Letters 366, Supplement_1 (2019): i127—i132. http://dx.doi.org/10.1093/femsle/fnz128s.
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ABSTRACT This study was conducted to evaluate the safety and bacterial profile of Dhanaan (Ethiopian traditional fermented camel milk). The composition of the microbial community in Dhanaan samples was analysed by a metagenomic approach of 16S rRNA gene amplicon sequencing. Metagenomic profiling identified 87 different bacterial microorganisms (OTUs) in six samples analysed. Although the Dhanaan samples contained various lactic acid bacteria (LAB), they also all contained undesirable microorganisms in large proportions. The following LAB genera were identified: Streptococcus, Lactococcus and Weissella. One Streptococcus species represented by OTU-1 (operational taxonomic unit) was found in all Dhanaan samples and the dominating species in four out of six samples. This common isolate was found to be closely related to S. lutetiensis and S. infantarius. Undesirable microorganisms from genera such as Escherichia, Klebsiella, Enterobacter, Acinetobacter and Clostridium were, however, also frequent, or even dominant in Dhanaan samples. Thus, this calls for a change in the Dahnaan manufacturing practice to an improved and safer production system. Starter cultures suitable for Dhanaan production might be developed from the Streptococcus, Weissella and Lactococcus microorganisms identified in this study. However, further safety evaluation and technological characterization need to be conducted on strains defined by OTU-1, OTU-2, OTU-3, OTU-8 and OTU-35 before they can be used as food grade starter cultures.
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Vollmar, Solveig, Robin Wellmann, Daniel Borda-Molina, Markus Rodehutscord, Amélia Camarinha-Silva, and Jörn Bennewitz. "The Gut Microbial Architecture of Efficiency Traits in the Domestic Poultry Model Species Japanese Quail (Coturnix japonica) Assessed by Mixed Linear Models." G3: Genes|Genomes|Genetics 10, no. 7 (2020): 2553–62. http://dx.doi.org/10.1534/g3.120.401424.
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It is well known that mammals and avian gut microbiota compositions are shaped by the host genomes and affect quantitative traits. The microbial architecture describes the impact of the microbiota composition on quantitative trait variation and the number and effect distribution of microbiota features. In the present study the gut microbial architecture of feed-related traits phosphorus and calcium utilization, daily gain, feed intake and feed per gain ratio in the domestic poultry model species Japanese quail were assessed by mixed linear models. The ileum microbiota composition was characterized by 16S rRNA amplicon sequencing techniques of growing individuals. The microbiability of the traits was on a similar level as the narrow sense heritability and was highly significant except for calcium utilization. The animal microbial correlation of the traits was substantial. Microbiome-wide association analyses revealed several traits associated and highly significant microbiota features, both on the bacteria genera as well as on the operational taxonomic unit level. Most features were significant for more than one trait, which explained the high microbial correlations. It can be concluded that the traits are polymicrobial determined with some microbiota features with larger effects and many with small effects. The results are important for the development of hologenomic selection schemes for feed-related traits in avian breeding programs that are targeting the host genome and the metagenome simultaneously.
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Cafà, Giovanni, Benedetta Caggiano, Michael A. Reeve, et al. "A Polyphasic Approach Aids Early Detection of Potentially Toxigenic Aspergilli in Soil." Microorganisms 7, no. 9 (2019): 300. http://dx.doi.org/10.3390/microorganisms7090300.
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Key chili and maize growing areas of Pakistan were selected for a focused baseline study of the levels of Aspergillus spp. Investigations were undertaken using a combination of molecular and culture-based techniques. Samples investigated included soil samples, one-year-old corn cobs, and fresh chili from selected locations. Aspergillus strains obtained from corn cobs were screened using coconut milk agar, resulting in one strain that was positive for aflatoxin production. Whole genome sequencing (WGS) with low coverage techniques were employed to screen the isolates for differences in the ribosomal RNA gene cluster and mitochondrial genome, with the aflatoxigenic strain proving to have a distinctive profile. Finally, strains were subjected to matrix-assisted laser-desorption and ionization time-of-flight mass spectrometry (MALDI-ToF-MS) in order to obtain a proteomic ‘fingerprint’ which was used to distinguish the aflatoxigenic strain from the other isolates. The next generation sequencing (NGS) study was broadened to incorporate metabarcoding with ITS rRNA for determining the microbial biodiversity of the soil samples and presumptive screening for the presence of aflatoxigenic strains. Using information gleaned from the WGS results, a putative aflatoxigenic operational taxonomic unit (OTU) was observed in four of the 15 soil samples screened by metabarcoding. This method may have beneficial applications in early detection and surveillance programs in agricultural soils and commodities.
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Asgari, Ehsaneddin, Philipp C. Münch, Till R. Lesker, Alice C. McHardy, and Mohammad R. K. Mofrad. "DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection." Bioinformatics 35, no. 14 (2018): 2498–500. http://dx.doi.org/10.1093/bioinformatics/bty954.
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Abstract Summary Identifying distinctive taxa for micro-biome-related diseases is considered key to the establishment of diagnosis and therapy options in precision medicine and imposes high demands on the accuracy of micro-biome analysis techniques. We propose an alignment- and reference- free subsequence based 16S rRNA data analysis, as a new paradigm for micro-biome phenotype and biomarker detection. Our method, called DiTaxa, substitutes standard operational taxonomic unit (OTU)-clustering by segmenting 16S rRNA reads into the most frequent variable-length subsequences. We compared the performance of DiTaxa to the state-of-the-art methods in phenotype and biomarker detection, using human-associated 16S rRNA samples for periodontal disease, rheumatoid arthritis and inflammatory bowel diseases, as well as a synthetic benchmark dataset. DiTaxa performed competitively to the k-mer based state-of-the-art approach in phenotype prediction while outperforming the OTU-based state-of-the-art approach in finding biomarkers in both resolution and coverage evaluated over known links from literature and synthetic benchmark datasets. Availability and implementation DiTaxa is available under the Apache 2 license at http://llp.berkeley.edu/ditaxa. Supplementary information Supplementary data are available at Bioinformatics online.
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Uriz, Maria J., Leire Garate, and Gemma Agell. "Molecular phylogenies confirm the presence of two crypticHemimycalespecies in the Mediterranean and reveal the polyphyly of the generaCrellaandHemimycale(Demospongiae: Poecilosclerida)." PeerJ 5 (March 7, 2017): e2958. http://dx.doi.org/10.7717/peerj.2958.
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BackgroundSponges are particularly prone to hiding cryptic species as their paradigmatic plasticity often favors species phenotypic convergence as a result of adaptation to similar habitat conditions.Hemimycaleis a sponge genus (Family Hymedesmiidae, Order Poecilosclerida) with four formally described species, from which onlyHemimycale columellahas been recorded in the Atlanto-Mediterranean basin, on shallow to 80 m deep bottoms. Contrasting biological features between shallow and deep individuals ofHemimycale columellasuggested larger genetic differences than those expected between sponge populations. To assess whether shallow and deep populations indeed belong to different species, we performed a phylogenetic study ofHemimycale columellaacross the Mediterranean. We also included otherHemimycaleandCrellaspecies from the Red Sea, with the additional aim of clarifying the relationships of the genusHemimycale.MethodsHemimycale columellawas sampled across the Mediterranean, and Adriatic Seas.Hemimycale arabicaandCrella cyathophorawere collected from the Red Sea and Pacific. From two to three specimens per species and locality were extracted, amplified for Cytochrome C Oxidase I (COI) (M1–M6 partition), 18S rRNA, and 28S (D3–D5 partition) and sequenced. Sequences were aligned using Clustal W v.1.81. Phylogenetic trees were constructed under neighbor joining (NJ), Bayesian inference (BI), and maximum likelihood (ML) criteria as implemented in Geneious software 9.01. Moreover, spicules of the target species were observed through a Scanning Electron microscope.ResultsThe several phylogenetic reconstructions retrieved bothCrellaandHemimycalepolyphyletic. Strong differences in COI sequences indicated thatC. cyathophorafrom the Red Sea might belong in a different genus, closer toHemimycale arabicathan to the Atlanto-MediterraneanCrellaspp. Molecular and external morphological differences betweenHemimycale arabicaand the Atlanto-MediterraneanHemimycalealso suggest thatHemimycale arabicafit in a separate genus. On the other hand, the Atlanto-Mediterranean Crellidae appeared in 18S and 28S phylogenies as a sister group of the Atlanto-MediterraneanHemimycale. Moreover, what was known up to now asHemimycale columella,is formed by two cryptic species with contrasting bathymetric distributions. Some small but consistent morphological differences allow species distinction.ConclusionsA new family (Hemimycalidae) including the genusHemimycaleand the two purported new genera receivingC. cyathophoraandHemimycale arabicamight be proposed according to our phylogenetic results. However, the inclusion of additional Operational Taxonomic Unit (OTUs) appears convenient before taking definite taxonomical decisions. A new cryptic species (Hemimycale mediterraneasp. nov.) is described. Morphologically undifferentiated species with contrasting biological traits, as those here reported, confirm that unidentified cryptic species may confound ecological studies.
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Wang, Yuchao, Ying Chen, Chao Wu, and Xiaohong Yang. "Informatic analysis of the pulmonary microecology in non-cystic fibrosis bronchiectasis at three different stages." Open Life Sciences 17, no. 1 (2022): 107–20. http://dx.doi.org/10.1515/biol-2022-0014.
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Abstract This study explored the impact of pulmonary microecological changes on disease progression in non-cystic fibrosis bronchiectasis (nCFB). A careful search of the NCBI BioProject database revealed the 16S rRNA-based microbiological testing results of 441 pulmonary sputum samples from patients in the relatively stable (baseline), acute exacerbation, or recovery stage. After preliminary analysis and screening, we selected 152 samples for further analyses, including determination of the operational taxonomic unit (OTU) distribution at the phylum, class, order, family and genus levels, community structure, alpha diversity, beta diversity, microbial multivariables, correlations, and community structure after the abundances of intragroup samples were averaged. The recovery group showed significant differences in pulmonary microbiological changes (P < 0.05) compared with the other groups. There were 30 differentially abundant OTUs, with 27 and 7 at the genus and phylum levels, respectively. The Chao1 value of the recovery group was comparable to that of the baseline group, and the Shannon and Simpson values of the recovery group were the highest. Rhodococcus in Actinobacteria was positively correlated with Ochrobactrum in Firmicutes. The differences in pulmonary microecological changes at different nCFB stages may serve as a biologically predictive indicator of nCFB progression.
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Cameron, Simon J. S., Arwyn Edwards, Robert J. Lambert, Mike Stroud, and Luis A. J. Mur. "Participants in the Trans-Antarctic Winter Traverse Expedition Showed Increased Bacterial Load and Diversity in Saliva but Maintained Individual Differences within Stool Microbiota and Across Metabolite Fingerprints." International Journal of Molecular Sciences 24, no. 5 (2023): 4850. http://dx.doi.org/10.3390/ijms24054850.
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Understanding the impact of long-term physiological and environmental stress on the human microbiota and metabolome may be important for the success of space flight. This work is logistically difficult and has a limited number of available participants. Terrestrial analogies present important opportunities to understand changes in the microbiota and metabolome and how this may impact participant health and fitness. Here, we present work from one such analogy: the Transarctic Winter Traverse expedition, which we believe is the first assessment of the microbiota and metabolome from different bodily locations during prolonged environmental and physiological stress. Bacterial load and diversity were significantly higher during the expedition when compared with baseline levels (p < 0.001) in saliva but not stool, and only a single operational taxonomic unit assigned to the Ruminococcaceae family shows significantly altered levels in stool (p < 0.001). Metabolite fingerprints show the maintenance of individual differences across saliva, stool, and plasma samples when analysed using flow infusion electrospray mass spectrometry and Fourier transform infrared spectroscopy. Significant activity-associated changes in terms of both bacterial diversity and load are seen in saliva but not in stool, and participant differences in metabolite fingerprints persist across all three sample types.
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Shi, YingWu, HongMei Yang, Ming Chu, et al. "Diversity and space–time dynamics of the bacterial communities in cotton (Gossypium hirsutum) rhizosphere soil." Canadian Journal of Microbiology 66, no. 3 (2020): 228–42. http://dx.doi.org/10.1139/cjm-2019-0196.
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Rhizosphere bacteria are key determinants of plant health and productivity. In this study, we used PCR-based next-generation sequencing to reveal the diversity and community composition of bacteria in the cotton rhizosphere from samples collected in Xinjiang Province, China. We identified 125 bacterial classes within 49 phyla from these samples. Proteobacteria (33.07% of total sequences), Acidobacteria (19.88%), and Gemmatimonadetes (11.19%) dominated the bacterial community. Marked differences were evident in the α-diversity of rhizosphere bacteria during different cotton plant growth and development stages. The operational taxonomic unit (OTU) numbers were highest in seedling and bud stages and decreased at the flowering and fruit-boll-opening stages. Forty-three OTUs from the Proteobacteria were common to all four periods of cotton development. Proteobacteria were more abundant in the rhizospheres of cotton from southern Xinjiang than from northern Xinjiang, while the opposite trend was observed for Acidobacteria. Gemmatimonadetes frequency was broadly the same in both northern and southern Xinjiang. These results suggest that there is abundant diversity in the microbiota of cotton rhizosphere soil. Proteobacteria and Actinobacteria dominated this microbial niche and bacterial communities in the seedling, bud, flowering, and boll-opening stages appear to be more similar to one another than to communities at the other growth stages.
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Torres, Jaire Marinho, Oliveira Carina Elisei De, Filipe Martins Santos, et al. "Trypanosomatid diversity in a bat community of an urban area in Campo Grande, Mato Grosso do Sul, Brazil." Infection, Genetics and Evolution 118 (June 12, 2024): 105563. https://doi.org/10.5281/zenodo.13427081.
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(Uploaded by Plazi for the Bat Literature Project) Bats have a long evolutionary history with trypanosomatids, but the role of these flying mammals on parasite transmission cycles in urban areas, especially for Trypanosoma and Leishmania species, remains poorly known. The objective of this study was to evaluate the species richness of trypanosomatids parasitizing a bat community in Campo Grande (CG), a state capital within the Cerrado of the Brazilian Midwest. We evaluated 237 bats of 13 species by means of hemoculture and molecular detection in spleen samples. The bat community of CG appears to participate in the transmission cycles of various species of trypanosomatids. We report an overall trypano somatid detection rate of 34.2% (n = 81), involving 11 out of 13 sampled bat species. We identified six species of trypanosomatids from 61 bats by analyzing SSU rRNA and/or kDNA: Trypanosoma cruzi DTU TcI, T. c. marinkellei, T. dionisii, Leishmania infantum, L. amazonensis, and T. janseni, with this latter being detected by hemoculture for the first time in a bat species. We also detected a Molecular Operational Taxonomic Unit, Trypanosoma sp. DID, in the phyllostomids Glossophaga soricina and Platyrrhinus lineatus. The highest trypanosomatid richness was observed for Sturnira lilium, which hosted three species: L. infantum, T. dionisii and T. janseni. Given that visceral leishmaniasis is endemic in CG, special focus should be placed on L. infantum. Moreover, L. amazonensis and T. cruzi warrant attention, since these are zoonotic parasites responsible for human cases of tegumentary leishmaniasis and Chagas disease, respectively. In this respect, we discuss how bat communities may influence the Leishmania spp. transmission in endemic areas.
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Torres, Jaire Marinho, Oliveira Carina Elisei De, Filipe Martins Santos, et al. "Trypanosomatid diversity in a bat community of an urban area in Campo Grande, Mato Grosso do Sul, Brazil." Infection, Genetics and Evolution 118 (June 7, 2024): 105563. https://doi.org/10.5281/zenodo.13427081.
Full textAbstract:
(Uploaded by Plazi for the Bat Literature Project) Bats have a long evolutionary history with trypanosomatids, but the role of these flying mammals on parasite transmission cycles in urban areas, especially for Trypanosoma and Leishmania species, remains poorly known. The objective of this study was to evaluate the species richness of trypanosomatids parasitizing a bat community in Campo Grande (CG), a state capital within the Cerrado of the Brazilian Midwest. We evaluated 237 bats of 13 species by means of hemoculture and molecular detection in spleen samples. The bat community of CG appears to participate in the transmission cycles of various species of trypanosomatids. We report an overall trypano somatid detection rate of 34.2% (n = 81), involving 11 out of 13 sampled bat species. We identified six species of trypanosomatids from 61 bats by analyzing SSU rRNA and/or kDNA: Trypanosoma cruzi DTU TcI, T. c. marinkellei, T. dionisii, Leishmania infantum, L. amazonensis, and T. janseni, with this latter being detected by hemoculture for the first time in a bat species. We also detected a Molecular Operational Taxonomic Unit, Trypanosoma sp. DID, in the phyllostomids Glossophaga soricina and Platyrrhinus lineatus. The highest trypanosomatid richness was observed for Sturnira lilium, which hosted three species: L. infantum, T. dionisii and T. janseni. Given that visceral leishmaniasis is endemic in CG, special focus should be placed on L. infantum. Moreover, L. amazonensis and T. cruzi warrant attention, since these are zoonotic parasites responsible for human cases of tegumentary leishmaniasis and Chagas disease, respectively. In this respect, we discuss how bat communities may influence the Leishmania spp. transmission in endemic areas.
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Feng, Chen, Junping Lu, Yongqin Jia, et al. "Changes in Freeze-Thaw Environments in a Cold Lake: Eliciting New Insights into the Activity and Composition of Bacterial Communities." Diversity 16, no. 6 (2024): 311. http://dx.doi.org/10.3390/d16060311.
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This study explored the dynamics of bacterial community composition, response to environmental factors, and co-occurrence network models across different habitats of Wuliangsuhai Lake during the glacial period. Water quality analysis and high-throughput sequencing were performed at 14 monitoring sites within the lake. Additionally, a co-occurrence network between the two bacterial operational taxonomic unit (OTU)-OTUs was established. The results indicated significant differences in water quality indices, namely total nitrogen (TN), chemical oxygen demand (COD), total dissolved solids (TDS), salinity (SAL), chlorophyll-a (Chl.a), and electrical conductivity (EC), between the ice bodies of Wuliangsuhai Lake and subglacial water. Although there were no significant differences in α diversity across various media, substantial differences were observed in β diversity. The VIF and RDA analyses revealed that lake water quality factors significantly affected the microbial community structure and COD and TDS had the highest explanation for the community composition change. Network analysis demonstrated that competition dominated the bacterial community in water bodies with higher complexity and stability and ice body bacteria exhibited more reciprocal relationships and weaker resistance to external environmental disturbances. The co-occurrence network demonstrated a modular structure in the external environment, with g_Flavobacterium, f_Arcobacteraceae, and g_Sphingobacteriaceae being the main keystone species. Investigating the habitat heterogeneity of lake bacterial communities and identifying major groups and key species using molecular ecological network models and their topological effects can provide a theoretical foundation for monitoring and assessing the structural stability of lake ecosystems in cold regions.