Phages - bacteria interactions network of the healthy human gut

AbstractWith an estimated 1031 particles on earth, bacteriophages are the most abundant genomic entities across all habitats and important drivers of microbial communities. Growing evidence suggest that they play roles in intestinal human microbiota homeostasis, and recent metagenomics studies on the viral fraction of this ecosystem have provided crucial information about their diversity and specificity. However, the bacterial hosts of this viral fraction, a necessary information to characterize further the balance of these ecosystems, remain poorly characterized. Here we unveil, using an enhanced metagenomic Hi-C approach, a large network of 6,651 host-phage relationships in the healthy human gut allowing to study in situ phage-host ratio. We notably found that half of these contigs appear to be sleeping prophages whereas ¼ exhibit a higher coverage than their associated MAG representing potentially active phages impacting the ecosystem. We also detect different candidate members of the crAss-like phage family as well as their bacterial hosts showing that these elusive phages infect different genus of Bacteroidetes. This work opens the door to single sample analysis and concomitant study of phages and bacteria in complex communities.

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MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut

eLife ◽

10.7554/elife.60608 ◽

2021 ◽

Vol 10 ◽

Author(s):

Martial Marbouty ◽

Agnès Thierry ◽

Gaël A Millot ◽

Romain Koszul

Keyword(s):

Dynamic Analysis ◽

Microbial Population ◽

High Specificity ◽

Mobile Genetic Elements ◽

Microbiota Composition ◽

Human Gut ◽

Bacterial Host ◽

Healthy Human ◽

Phage Sequence

Bacteriophages play important roles in regulating the intestinal human microbiota composition, dynamics, and homeostasis, and characterizing their bacterial hosts is needed to understand their impact. We applied a metagenomic Hi-C approach on 10 healthy human gut samples to unveil a large infection network encompassing more than 6000 interactions bridging a metagenomic assembled genomes (MAGs) and a phage sequence, allowing to study in situ phage-host ratio. Whereas three-quarters of these sequences likely correspond to dormant prophages, 5% exhibit a much higher coverage than their associated MAG, representing potentially actively replicating phages. We detected 17 sequences of members of the crAss-like phage family, whose hosts diversity remained until recently relatively elusive. For each of them, a unique bacterial host was identified, all belonging to different genus of Bacteroidetes. Therefore, metaHiC deciphers infection network of microbial population with a high specificity paving the way to dynamic analysis of mobile genetic elements in complex ecosystems.

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Influence of pig farming on human Gut Microbiota: role of airborne microbial communities

Gut Microbes ◽

10.1080/19490976.2021.1927634 ◽

2021 ◽

Vol 13 (1) ◽

pp. 1-13

Author(s):

Julia Moor ◽

Tsering Wüthrich ◽

Suzanne Aebi ◽

Nadezda Mostacci ◽

Gudrun Overesch ◽

...

Keyword(s):

Gut Microbiota ◽

Microbial Communities ◽

Human Gut ◽

Human Gut Microbiota ◽

Pig Farming

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Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn’s Disease

Cellular and Molecular Gastroenterology and Hepatology ◽

10.1016/j.jcmgh.2016.05.011 ◽

2016 ◽

Vol 2 (5) ◽

pp. 563-566.e5 ◽

Cited By ~ 11

Author(s):

Chandra Sekhar Pedamallu ◽

Ami S. Bhatt ◽

Susan Bullman ◽

Sharyle Fowler ◽

Samuel S. Freeman ◽

...

Keyword(s):

Crohn’S Disease ◽

Crohn's Disease ◽

Microbial Communities

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Screening and Isolation of Bacterial Strains with the Biotechnological Potential to Destruct Cyanide-Bearing Compounds under the Conditions of Extreme Continental Climate

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.1130.19 ◽

2015 ◽

Vol 1130 ◽

pp. 19-22

Author(s):

M.P. Belykh ◽

S.V. Petrov ◽

V.F. Petrov ◽

A.Yu. Chikin ◽

N.L. Belkova

Keyword(s):

Microbial Communities ◽

Gold Mining ◽

Molecular Genetic ◽

Heap Leaching ◽

Bacterial Strains ◽

Mining Operations ◽

Biotechnological Potential ◽

Enriched Cultures ◽

Continental Climate

The methods of biodegradation are of special interest because they help solving environmental problems of wastes detoxification from gold-mining operations. The use of bacterial strains is a promising approach in the field of biotechnology to destruct cyanide-bearing compounds. The diversity of microbial communities both in heap in situ and in the enriched cultures was studied with molecular genetic methods. The differences in representation of bacteria, cultivated in unexploitable and operating heaps, are territory, site and heap specific. The strains of Pseudomonas sp. and Methylobacterium sp. possess the biotechnological potential and might be used in biodegradation of heap leaching wastes in extreme continental climate.

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Enzymatic Degradation of Phenazines Can Generate Energy and Protect Sensitive Organisms from Toxicity

mBio ◽

10.1128/mbio.01520-15 ◽

2015 ◽

Vol 6 (6) ◽

Cited By ~ 26

Author(s):

Kyle C. Costa ◽

Megan Bergkessel ◽

Scott Saunders ◽

Jonas Korlach ◽

Dianne K. Newman

Keyword(s):

Microbial Communities ◽

Pathogenic Fungi ◽

Cell Types ◽

Redox Activity ◽

Mycobacterium Fortuitum ◽

Active Metabolites ◽

Content Type ◽

Phenazine Production ◽

Physiological Benefits

ABSTRACTDiverse bacteria, including severalPseudomonasspecies, produce a class of redox-active metabolites called phenazines that impact different cell types in nature and disease. Phenazines can affect microbial communities in both positive and negative ways, where their presence is correlated with decreased species richness and diversity. However, little is known about how the concentration of phenazines is modulatedin situand what this may mean for the fitness of members of the community. Through culturing of phenazine-degrading mycobacteria, genome sequencing, comparative genomics, and molecular analysis, we identified several conserved genes that are important for the degradation of threePseudomonas-derived phenazines: phenazine-1-carboxylic acid (PCA), phenazine-1-carboxamide (PCN), and pyocyanin (PYO). PCA can be used as the sole carbon source for growth by these organisms. Deletion of several genes inMycobacterium fortuitumabolishes the degradation phenotype, and expression of two genes in a heterologous host confers the ability to degrade PCN and PYO. In cocultures with phenazine producers, phenazine degraders alter the abundance of different phenazine types. Not only does degradation support mycobacterial catabolism, but also it provides protection to bacteria that would otherwise be inhibited by the toxicity of PYO. Collectively, these results serve as a reminder that microbial metabolites can be actively modified and degraded and that these turnover processes must be considered when the fate and impact of such compounds in any environment are being assessed.IMPORTANCEPhenazine production byPseudomonasspp. can shape microbial communities in a variety of environments ranging from the cystic fibrosis lung to the rhizosphere of dryland crops. For example, in the rhizosphere, phenazines can protect plants from infection by pathogenic fungi. The redox activity of phenazines underpins their antibiotic activity, as well as providing pseudomonads with important physiological benefits. Our discovery that soil mycobacteria can catabolize phenazines and thereby protect other organisms against phenazine toxicity suggests that phenazine degradation may influence turnoverin situ. The identification of genes involved in the degradation of phenazines opens the door to monitoring turnover in diverse environments, an essential process to consider when one is attempting to understand or control communities influenced by phenazines.

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In situ analysis of native microbial communities in complex samples with high particulate loads

FEMS Microbiology Letters ◽

10.1016/j.femsle.2005.09.018 ◽

2005 ◽

Vol 253 (1) ◽

pp. 55-58 ◽

Cited By ~ 84

Author(s):

Anna Barra Caracciolo ◽

Paola Grenni ◽

Cinzia Cupo ◽

Simona Rossetti

Keyword(s):

Microbial Communities ◽

In Situ Analysis ◽

Complex Samples ◽

Particulate Loads

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Baseline human gut microbiota profile in healthy people and standard reporting template

10.1101/445353 ◽

2018 ◽

Author(s):

Charles Hadley King ◽

Hiral Desai ◽

Allison C. Sylvetsky ◽

Jonathan LoTempio ◽

Shant Ayanyan ◽

...

Keyword(s):

Dark Matter ◽

Regulatory Agencies ◽

Fecal Transplant ◽

Human Gut ◽

Healthy Human ◽

Comprehensive Knowledge ◽

Analysis Workflow ◽

Standard Report ◽

Abundance Profile ◽

Microbiome Data

A comprehensive knowledge of the types and ratios of microbes that inhabit the healthy human gut is necessary before any kind of pre-clinical or clinical study can be performed that attempts to alter the microbiome to treat a condition or improve therapy outcome. To address this need we present an innovative scalable comprehensive analysis workflow, a healthy human reference microbiome list and abundance profile (GutFeelingKB), and a novel Fecal Biome Population Report (FecalBiome) with clinical applicability. GutFeelingKB provides a list of 157 organisms (8 phyla, 18 classes, 23 orders, 38 families, 59 genera and 109 species) that forms the baseline biome and therefore can be used as healthy controls for studies related to dysbiosis. The incorporation of microbiome science into routine clinical practice necessitates a standard report for comparison of an individual’s microbiome to the growing knowledgebase of “normal” microbiome data. The FecalBiome and the underlying technology of GutFeelingKB address this need. The knowledgebase can be useful to regulatory agencies for the assessment of fecal transplant and other microbiome products, as it contains a list of organisms from healthy individuals. In addition to the list of organisms and abundances the study also generated a list of contigs of metagenomics dark matter. In this study, metagenomic dark matter represents sequences that cannot be mapped to any known sequence but can be assembled into contigs of 10,000 nucleotides or higher. These sequences can be used to create primers to study potential novel organisms. All data is freely available from https://hive.biochemistry.gwu.edu/gfkb and NCBI’s Short Read Archive.

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Enterotype Variations of the Healthy Human Gut Microbiome in Different Geographical Regions

Bioinformation ◽

10.6026/97320630014560 ◽

2018 ◽

Vol 14 (9) ◽

pp. 560-573 ◽

Cited By ~ 7

Author(s):

Fauzul Mobeen ◽

◽

Vikas Sharma ◽

Tulika Prakash ◽

◽

...

Keyword(s):

Gut Microbiome ◽

Human Gut ◽

Healthy Human ◽

Human Gut Microbiome ◽

Geographical Regions

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MICROBIAL CONTROL OF LIVE/DEAD ZOOPLANKTON RATIO IN SEVASTOPOL BAY

Ecologica Montenegrina ◽

10.37828/em.2017.11.9 ◽

2017 ◽

Vol 11 ◽

pp. 42-48 ◽

Cited By ~ 1

Author(s):

Vladimir S. Mukhanov ◽

Daria Litvinyuk

Keyword(s):

Water Pollution ◽

Microbial Communities ◽

Decomposition Rate ◽

Microbial Control ◽

Mortality Rates ◽

Pollution Status ◽

Sevastopol Bay ◽

In Situ Decomposition ◽

Bacterioplankton Abundance

To explain higher fraction of live zooplankton in heavily polluted and eutrophic Sevastopol Bay comparing with cleaner adjacent waters, a hypothesis has been proposed and tested experimentally that more intensive bacteria-driven decomposition of dead organisms in the bay reduced their pool and, as a result, increased the live-to-dead zooplankton ratio. In the experiment, a heat-killed batch culture of the copepod Calanipeda aquaedulcis was used as a substrate for decomposition by natural microbial communities from the waters of different pollution status. Bacterioplankton abundance and in situ decomposition rate of copepod carcasses were shown to be about 3-fold higher in the bay (1.3 × 106 cells ml-1 and 0.13 day-1, respectively) while an approximation of zooplankton non-predatory mortality rates gave equal values for both the sites (about 0.046 day-1). These findings call for revising the ways of interpreting the results of zooplankton viability assays in their relation to water pollution status.

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Combined Microautoradiography–16S rRNA Probe Technique for Determination of Radioisotope Uptake by Specific Microbial Cell Types In Situ

Applied and Environmental Microbiology ◽

10.1128/aem.65.4.1746-1752.1999 ◽

1999 ◽

Vol 65 (4) ◽

pp. 1746-1752 ◽

Cited By ~ 237

Author(s):

Cleber C. Ouverney ◽

Jed A. Fuhrman

Keyword(s):

In Situ Hybridization ◽

16S Rrna ◽

Microbial Communities ◽

Fluorescent In Situ Hybridization ◽

Amino Acid Uptake ◽

Cell Types ◽

Black Box ◽

Acid Uptake ◽

Substrate Uptake

ABSTRACT We propose a novel method for studying the function of specific microbial groups in situ. Since natural microbial communities are dynamic both in composition and in activities, we argue that the microbial “black box” should not be regarded as homogeneous. Our technique breaks down this black box with group-specific fluorescent 16S rRNA probes and simultaneously determines 3H-substrate uptake by each of the subgroups present via microautoradiography (MAR). Total direct counting, fluorescent in situ hybridization, and MAR are combined on a single slide to determine (i) the percentages of different subgroups in a community, (ii) the percentage of total cells in a community that take up a radioactively labeled substance, and (iii) the distribution of uptake within each subgroup. The method was verified with pure cultures. In addition, in situ uptake by members of the α subdivision of the class Proteobacteria(α-Proteobacteria) and of the Cytophaga-Flavobacteriumgroup obtained off the California coast and labeled with fluorescent oligonucleotide probes for these subgroups showed that not only do these organisms account for a large portion of the picoplankton community in the sample examined (∼60% of the universal probe-labeled cells and ∼50% of the total direct counts), but they also are significant in the uptake of dissolved amino acids in situ. Nearly 90% of the total cells and 80% of the cells belonging to the α-Proteobacteria and Cytophaga-Flavobacterium groups were detectable as active organisms in amino acid uptake tests. We suggest a name for our triple-labeling technique, substrate-tracking autoradiographic fluorescent in situ hybridization (STARFISH), which should aid in the “dissection” of microbial communities by type and function.

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