Functional features of microbial communities in the digestive tract of field voles (Microtus rossiaemeridionalis and Clethrionomys glareolus)

AbstractAlthough numerous metagenome, amplicon sequencing-based studies have been conducted to date to characterize marine microbial communities, relatively few have employed full metagenome shotgun sequencing to obtain a broader picture of the functional features of these marine microbial communities. Moreover, most of these studies only performed sporadic sampling, which is insufficient to understand an ecosystem comprehensively. In this study, we regularly conducted seawater sampling along the northeastern Pacific coast of Japan between March 2012 and May 2016. We collected 213 seawater samples and prepared size-based fractions to generate 454 subsets of samples for shotgun metagenome sequencing and analysis. We also determined the sequences of 16S rRNA (n = 111) and 18S rRNA (n = 47) gene amplicons from smaller sample subsets. We thereafter developed the Ocean Monitoring Database for time-series metagenomic data (http://marine-meta.healthscience.sci.waseda.ac.jp/omd/), which provides a three-dimensional bird’s-eye view of the data. This database includes results of digital DNA chip analysis, a novel method for estimating ocean characteristics such as water temperature from metagenomic data. Furthermore, we developed a novel classification method that includes more information about viruses than that acquired using BLAST. We further report the discovery of a large number of previously overlooked (TAG)n repeat sequences in the genomes of marine microbes. We predict that the availability of this time-series database will lead to major discoveries in marine microbiome research.

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Gluten-degrading bacteria: availability and applications

Applied Microbiology and Biotechnology ◽

10.1007/s00253-021-11263-5 ◽

2021 ◽

Author(s):

Viia Kõiv ◽

Tanel Tenson

Keyword(s):

Microbial Communities ◽

Digestive Tract ◽

Storage Proteins ◽

Gluten Free Diet ◽

Natural Food ◽

Gluten Free ◽

Efficient Treatment ◽

Gluten Intolerance ◽

Degrading Bacteria ◽

Human Digestive Tract

Abstract Gluten is a mixture of storage proteins in wheat and occurs in smaller amounts in other cereal grains. It provides favorable structure to bakery products but unfortunately causes disease conditions with increasing prevalence. In the human gastrointestinal tract, gluten is cleaved into proline and gluten rich peptides that are not degraded further. These peptides trigger immune responses that might lead to celiac disease, wheat allergy, and non-celiac gluten sensitivity. The main treatment option is a gluten-free diet. Alternatively, using enzymes or microorganisms with gluten-degrading properties might alleviate the disease. These components can be used during food production or could be introduced into the digestive tract as food supplements. In addition, natural food from the environment is known to enrich the microbial communities in gut and natural environmental microbial communities have high potential to degrade gluten. It remains to be investigated if food and environment-induced changes in the gut microbiome could contribute to the triggering of gluten-related diseases. Key points • Wheat proteins, gluten, are incompletely digested in human digestive tract leading to gluten intolerance. • The only efficient treatment of gluten intolerance is life-long gluten-free diet. • Environmental bacteria acquired together with food could be source of gluten-degrading bacteria detoxifying undigested gluten peptides.

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Composition of the microbial communities in the gastrointestinal tract of perch ( Perca fluviatilis L. 1758) and cestodes parasitizing the perch digestive tract

Journal of Fish Diseases ◽

10.1111/jfd.13096 ◽

2019 ◽

Vol 43 (1) ◽

pp. 23-38 ◽

Cited By ~ 1

Author(s):

Elena N. Kashinskaya ◽

Evgeniy P. Simonov ◽

Galina I. Izvekova ◽

Aleksey N. Parshukov ◽

Karl B. Andree ◽

...

Keyword(s):

Gastrointestinal Tract ◽

Microbial Communities ◽

Digestive Tract ◽

Perca Fluviatilis ◽

Perch Perca Fluviatilis

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Complete Genome Sequence of Streptococcus salivarius HSISS4, a Human Commensal Bacterium Highly Prevalent in the Digestive Tract

Genome Announcements ◽

10.1128/genomea.01637-15 ◽

2016 ◽

Vol 4 (1) ◽

Cited By ~ 4

Author(s):

Johann Mignolet ◽

Laetitia Fontaine ◽

Michiel Kleerebezem ◽

Pascal Hols

Keyword(s):

Small Intestine ◽

Microbial Communities ◽

Digestive Tract ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Streptococcus Salivarius ◽

Commensal Bacterium ◽

Circular Chromosome ◽

Coding Sequences

The human commensal bacterium Streptococcus salivarius plays a major role in the equilibrium of microbial communities of the digestive tract. Here, we report the first complete genome sequence of a Streptococcus salivarius strain isolated from the small intestine, namely, HSISS4. Its circular chromosome comprises 1,903 coding sequences and 2,100,988 nucleotides.

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Biological activity of soils in the settlements of southern (Microtus rossiaemeridionalis) and bank (Clethrionomys glareolus) voles

Biology Bulletin ◽

10.1134/s1062359013040110 ◽

2014 ◽

Vol 41 (1) ◽

pp. 80-88 ◽

Cited By ~ 6

Author(s):

E. S. Manaeva ◽

N. O. Lomovtseva ◽

N. V. Kostina ◽

M. V. Gorlenko ◽

M. M. Umarov

Keyword(s):

Biological Activity ◽

Clethrionomys Glareolus ◽

Microtus Rossiaemeridionalis

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Cloacal swabs and alcohol bird specimens are good proxies for compositional analyses of gut microbial communities of Great tits (Parus major)

10.21203/rs.2.19814/v2 ◽

2020 ◽

Author(s):

Kasun H Bodawatta ◽

Katerina Puzejova ◽

Katerina Sam ◽

Michael Poulsen ◽

Knud A. Jønsson

Keyword(s):

Microbial Communities ◽

Digestive Tract ◽

Wild Bird ◽

Anthropogenic Impacts ◽

Parus Major ◽

Amplicon Sequencing ◽

Cloacal Swab ◽

Non Invasive ◽

16S Rrna Amplicon Sequencing ◽

Microbiome Research

Abstract Background Comprehensive studies of wild bird microbiomes are often limited by difficulties of sample acquisition. However, widely used non-invasive cloacal swab methods and under-explored museum specimens preserved in alcohol provide promising avenues to increase our understanding of wild bird microbiomes, provided that they accurately portray natural microbial community compositions. To investigate this assertion, we used 16S rRNA amplicon sequencing of Great tit (Parus major) gut microbiomes to compare 1) microbial communities obtained from dissected digestive tract regions and cloacal swabs, and 2) microbial communities obtained from freshly dissected gut regions and from samples preserved in alcohol for two weeks or two months, respectively. Results We found no significant differences in alpha diversities in communities of different gut regions and cloacal swabs (except in OTU richness between the dissected cloacal region and the cloacal swabs), or between fresh and alcohol preserved samples. However, we did find significant differences in beta diversity and community composition of cloacal swab samples compared to different gut regions. Despite these community-level differences, swab samples qualitatively captured the majority of the bacterial diversity throughout the gut better than any single compartment. Bacterial community compositions of alcohol-preserved specimens did not differ significantly from freshly dissected samples, although some low-abundant taxa were lost in the alcohol preserved specimens. Conclusions Our findings suggest that cloacal swabs, similar to non-invasive fecal sampling, qualitatively depict the gut microbiota composition without having to collect birds to extract the full digestive tract. Secondly, the satisfactory depiction of gut microbial communities in alcohol preserved samples opens up for the possibility of using an enormous resource readily available through museum collections to characterize bird gut microbiomes. The use of extensive museum specimen collections of birds for microbial gut analyses would allow for investigations of temporal patterns of wild bird gut microbiomes, including the potential effects of climate change and anthropogenic impacts. Overall, the utilization of cloacal swabs and museum alcohol specimens can positively impact bird gut microbiome research to help increase our understanding of the role and evolution of wild bird hosts and gut microbial communities.

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Localization of bacterial communities within gut compartments across Cephalotes turtle ants

Applied and Environmental Microbiology ◽

10.1128/aem.02803-20 ◽

2021 ◽

Author(s):

Peter J. Flynn ◽

Catherine L. D’Amelio ◽

Jon G. Sanders ◽

Jacob A. Russell ◽

Corrie S. Moreau

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Digestive Tract ◽

Bacterial Communities ◽

Evolutionary History ◽

Amplicon Sequencing ◽

Caste Differentiation ◽

Animal Group ◽

16S Rrna Amplicon Sequencing ◽

Host Phylogeny

Microbial communities within the animal digestive tract often provide important functions for their hosts. The composition of eukaryotes' gut bacteria can be shaped by host diet, vertical bacterial transmission, and physiological variation within the digestive tract. In several ant taxa, recent findings have demonstrated that nitrogen provisioning by symbiotic bacteria makes up for deficiencies in herbivorous diets. Using 16S rRNA amplicon sequencing and qPCR, this study examined bacterial communities at a fine scale across one such animal group, the turtle ant genus Cephalotes. We analyzed the composition and colonization density across four portions of the digestive tract to understand how bacterial diversity is structured across gut compartments, potentially allowing for specific metabolic functions of benefit to the host. In addition, we aimed to understand if caste differentiation or host relatedness influences the gut bacterial communities of Cephalotes ants. Microbial communities were found to vary strongly across Cephalotes gut compartments in ways that transcend both caste and host phylogeny. Despite this, caste and host phylogeny still have detectable effects. We demonstrated microbial community divergence across gut compartments, possibly due to the varying function of each gut compartment for digestion. IMPORTANCE Gut compartments play an important role in structuring the microbial community within individual ants. The gut chambers of the turtle ant digestive tract differ remarkably in symbiont abundance and diversity. Furthermore, caste type explains some variation in the microbiome composition. Finally, the evolutionary history of the Cephalotes species structures the microbiome in our study, which elucidates a trend in which related ants maintain related microbiomes, conceivably owing to co-speciation. Amazingly, gut compartment-specific signatures of microbial diversity, relative abundance, composition, and abundance have been conserved over Cephalotes evolutionary history, signifying that this symbiosis has been largely stable for over 50 million years.

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Peanut/Cotton Intercropping Increases Productivity and Economic Returns by Regulating Nutrient Accumulation and Soil Microbial Communities Under both Normal and Saline Soil Conditions

10.21203/rs.3.rs-1145699/v1 ◽

2021 ◽

Author(s):

Wei Xie ◽

Kai Zhang ◽

Xiaoying Wang ◽

Xiaoxia Zou ◽

Xiaojun Zhang ◽

...

Keyword(s):

Microbial Communities ◽

Crop Yield ◽

Bacterial Abundance ◽

Saline Soil ◽

Soil Microbial Communities ◽

Soil Conditions ◽

Nutrient Accumulation ◽

Economic Returns ◽

Soil Microbial ◽

Functional Features

Abstract Background Intercropping has been widely adopted by farmers for it often enhances crop productivity and economic returns; however, the underpinning mechanisms from the perspective of belowground interspecific interactions are only partly understood especially when intercropping under saline soil conditions. By using permeable (100 µm) and impermeable (solid) root barriers in a multi-site field experiment, we aimed to study the impact of root-root interactions on nutrient accumulation, soil microbial communities, crop yield, and economic returns in a peanut/cotton intercropping system under non-saline, secondary-saline, and coastal saline soil conditions. Results The results indicate that intercropping (IC) decreased the peanut pods yield while increased the seed cotton yield, and consequently enhanced the economic returns compared with monoculture of peanut (MP) and cotton (MC). The higher accumulations of nutrients such as nitrogen (N), phosphorus (P), and potassium (K) were also observed in IC not only in the soil but also in vegetative tissues and reproductive organs. Bacterial community structure analysis under normal growth conditions reveals that IC dramatically altered the soil bacterial abundance composition in both peanut and cotton strips of the top soil whereas the bacterial diversity was barely affected compared with MP and MC. At blossom-needling stage, the metabolic functional features of the bacterial communities such as fatty acid biosynthesis, lipoic acid metabolism, peptidoglycan biosynthesis, and biosynthesis of ansamycins were significantly enriched in MP compared with other treatments. Conversely, these metabolic functional features were dramatically depleted in MP while significantly enriched in IC at podding stage. Permeable root barrier treatments (NC-P and NC-C) counteracted the benefits of IC and the side effects were more pronounced in impermeable treatments (SC-P and SC-C). Conclusion Peanut/cotton intercropping increases crop yield as well as economic returns under non-saline, secondary-saline, and coastal saline soil conditions probably by modulating the soil bacterial abundance composition and accelerating nutrients accumulation.

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Microbiological Approach to Reconstruction of the Original Content of Pots from the Burials

Nizhnevolzhskiy Arheologicheskiy Vestnik ◽

10.15688/nav.jvolsu.2020.1.10 ◽

2020 ◽

pp. 188-201

Author(s):

Tatiana Khomutova ◽

Kamilla Dushchanova ◽

Alexandr Borisov

Keyword(s):

Microbial Biomass ◽

Microbial Communities ◽

Bronze Age ◽

Carboxylic Acids ◽

Soil Microbial Communities ◽

Bottom Layer ◽

Organic Substrates ◽

Microbial Decomposition ◽

Functional Features ◽

Multisubstrate Testing

In a model soil experiment, microbial decomposition nature and its rate applying to various organic substrates were studied. It is shown that the decomposition of various materials changes the functional features of microbial communities. These changes are assessed using multisubstrate testing of respiratory activity of microbial communities – this testing assumes application of low- molecular respiratory inducers (aminoacids and carboxylic acids) to the soil and registration the changes of the intensity of carbon dioxide release by microorganisms. Indicative compounds such as ascorbate, lactate, acetate (from the group of carboxylic acid salts) and cysteine (from the group of aminoacids) have been identified to be promising for use in reconstructing the original contents of ritual vessels. As an example, the article presents the results of reconstruction of one of bronze age burial pots original content, obtained by multisubstrate testing. High microbial biomass in the bottom layer of the vessel and the specific microbial communities’ respiratory responses to carboxylic acids salts (ascorbate, lactate and acetate) and aminoacid cysteine addition, indicate that the vessel originally contained a nutritional product, the decomposition of which led both to increase of microbial biomass and to changes in the functional structure of microbial community in the soil filling of the bottom layer. The results of statistical analysis of the reactions of soil microbial communities from the pot and from soils of the model experiment with known materials decomposed indicate that the vessel initially contained a protein product with a possible component of oil and starch.

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