scholarly journals Ecological Stability Emerges at the Level of Strains in the Human Gut Microbiome

2021 ◽  
Author(s):  
Richard Wolff ◽  
William R. Shoemaker ◽  
Nandita R. Garud
Keyword(s):  
Gut Microbiome ◽  
Species Abundance ◽  
Species Level ◽  
Strain Level ◽  
Ecological Stability ◽  
Human Gut ◽  
Healthy Human ◽  
Human Gut Microbiome ◽  
Abundance Fluctuations ◽  
Over Time

The human gut microbiome is a complex community that harbors substantial ecological diversity at the species level, as well as at the strain level within species. In healthy hosts, species abundance fluctuations in the microbiome community are thought to be stable, and these fluctuations can be described by macroecological laws. However, it is less clear how strain abundances change over time. An open question is whether individual strains behave like species themselves, exhibiting stability and following the macroecological relationships known to hold at the species level, or whether strains have different dynamics, perhaps due to the relatively close phylogenetic relatedness of co-colonizing lineages. In this study, we sought to characterize the typical strain-level dynamics of the healthy human gut microbiome on timescales ranging from days to years. We show that genetic diversity within almost all species is stationary, tending towards a long-term typical value within hosts over time scales of several years, despite fluctuations on shorter timescales. Moreover, the abundance fluctuations of strains can be sufficiently described by a stochastic logistic model (SLM), a model previously used to describe abundance fluctuations among species around a fixed carrying capacity, in the vast majority of cases, suggesting that strains are dynamically stable. Lastly, we find that strain abundances follow the same macroecological laws known to hold at the species level. Together, our results suggest that macroecological properties of the human gut microbiome, including its stability, emerge at the level of strains.

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

2018 ◽  
Vol 14 (9) ◽  
pp. 560-573 ◽  
Author(s):  
Fauzul Mobeen ◽  
◽  
Vikas Sharma ◽  
Tulika Prakash ◽  
◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Human Gut ◽  
Healthy Human ◽  
Human Gut Microbiome ◽  
Geographical Regions

scholarly journals Defining a Healthy Human Gut Microbiome: Current Concepts, Future Directions, and Clinical Applications

2012 ◽  
Vol 12 (5) ◽  
pp. 611-622 ◽  
Author(s):  
Fredrik Bäckhed ◽  
Claire M. Fraser ◽  
Yehuda Ringel ◽  
Mary Ellen Sanders ◽  
R. Balfour Sartor ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Clinical Applications ◽  
Human Gut ◽  
Healthy Human ◽  
Future Directions ◽  
Human Gut Microbiome

scholarly journals Systematic characterization of human gut microbiome-secreted molecules by integrated multi-omics

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Bianca De Saedeleer ◽  
Antoine Malabirade ◽  
Javier Ramiro-Garcia ◽  
Janine Habier ◽  
Jean-Pierre Trezzi ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Complex Mixture ◽  
Host Cells ◽  
Methodological Framework ◽  
Secretion Systems ◽  
Human Gut ◽  
Healthy Human ◽  
Human Gut Microbiome ◽  
Health And Disease

AbstractThe human gut microbiome produces a complex mixture of biomolecules that interact with human physiology and play essential roles in health and disease. Crosstalk between micro-organisms and host cells is enabled by different direct contacts, but also by the export of molecules through secretion systems and extracellular vesicles. The resulting molecular network, comprised of various biomolecular moieties, has so far eluded systematic study. Here we present a methodological framework, optimized for the extraction of the microbiome-derived, extracellular biomolecular complement, including nucleic acids, (poly)peptides, and metabolites, from flash-frozen stool samples of healthy human individuals. Our method allows simultaneous isolation of individual biomolecular fractions from the same original stool sample, followed by specialized omic analyses. The resulting multi-omics data enable coherent data integration for the systematic characterization of this molecular complex. Our results demonstrate the distinctiveness of the different extracellular biomolecular fractions, both in terms of their taxonomic and functional composition. This highlights the challenge of inferring the extracellular biomolecular complement of the gut microbiome based on single-omic data. The developed methodological framework provides the foundation for systematically investigating mechanistic links between microbiome-secreted molecules, including those that are typically vesicle-associated, and their impact on host physiology in health and disease.

scholarly journals A transomic cohort as a reference point for promoting a healthy human gut microbiome

2021 ◽  
pp. 100039
Author(s):  
Zhuye Jie ◽  
Suisha Liang ◽  
Qiuxia Ding ◽  
Fei Li ◽  
Shanmei Tang ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Reference Point ◽  
Human Gut ◽  
Healthy Human ◽  
Human Gut Microbiome

scholarly journals The Human Gut Phageome: Origins and Roles in the Human Gut Microbiome

2021 ◽  
Vol 11 ◽  
Author(s):  
Eleanor M. Townsend ◽  
Lucy Kelly ◽  
George Muscatt ◽  
Joshua D. Box ◽  
Nicole Hargraves ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Adult Life ◽  
Microbial Populations ◽  
Human Gut ◽  
Bacterial Populations ◽  
Human Gut Microbiome ◽  
Microbiome Research ◽  
Health And Disease ◽  
Over Time

The investigation of the microbial populations of the human body, known as the microbiome, has led to a revolutionary field of science, and understanding of its impacts on human development and health. The majority of microbiome research to date has focussed on bacteria and other kingdoms of life, such as fungi. Trailing behind these is the interrogation of the gut viruses, specifically the phageome. Bacteriophages, viruses that infect bacterial hosts, are known to dictate the dynamics and diversity of bacterial populations in a number of ecosystems. However, the phageome of the human gut, while of apparent importance, remains an area of many unknowns. In this paper we discuss the role of bacteriophages within the human gut microbiome. We examine the methods used to study bacteriophage populations, how this evolved over time and what we now understand about the phageome. We review the phageome development in infancy, and factors that may influence phage populations in adult life. The role and action of the phageome is then discussed at both a biological-level, and in the broader context of human health and disease.

scholarly journals Comparative Genomics Guides Elucidation of Vitamin B12 Biosynthesis in Novel Human-Associated Akkermansia Strains

2019 ◽  
Vol 86 (3) ◽  
Author(s):  
Nina Kirmiz ◽  
Kadir Galindo ◽  
Karissa L. Cross ◽  
Estefani Luna ◽  
Nicholas Rhoades ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Species Level ◽  
Vitamin B ◽  
Human Gut ◽  
Content Type ◽  
Human Host ◽  
Akkermansia Muciniphila ◽  
Human Gut Microbiome ◽  
Physiological Diversity ◽  
Bacterial Lineage

ABSTRACT Akkermansia muciniphila is a mucin-degrading bacterium found in the gut of most humans and is considered a “next-generation probiotic.” However, knowledge of the genomic and physiological diversity of human-associated Akkermansia sp. strains is limited. Here, we reconstructed 35 metagenome-assembled genomes and combined them with 40 publicly available genomes for comparative genomic analysis. We identified at least four species-level phylogroups (AmI to AmIV), with distinct functional potentials. Most notably, we identified genes for cobalamin (vitamin B12) biosynthesis within the AmII and AmIII phylogroups. To verify these predictions, 10 Akkermansia strains were isolated from adults and screened for vitamin B12 biosynthesis genes via PCR. Two AmII strains were positive for the presence of cobalamin biosynthesis genes, while all 9 AmI strains tested were negative. To demonstrate vitamin B12 biosynthesis, we measured the production of acetate, succinate, and propionate in the presence and absence of vitamin supplementation in representative strains of the AmI and AmII phylogroups, since cobalamin is an essential cofactor in propionate metabolism. Results showed that the AmII strain produced acetate and propionate in the absence of supplementation, which is indicative of vitamin B12 biosynthesis. In contrast, acetate and succinate were the main fermentation products for the AmI strains when vitamin B12 was not supplied in the culture medium. Lastly, two bioassays were used to confirm vitamin B12 production by the AmII phylogroup. This novel physiological trait of human-associated Akkermansia strains may affect how these bacteria interact with the human host and other members of the human gut microbiome. IMPORTANCE There is significant interest in the therapeutic and probiotic potential of the common gut bacterium Akkermansia muciniphila. However, knowledge of both the genomic and physiological diversity of this bacterial lineage is limited. Using a combination of genomic, molecular biological, and traditional microbiological approaches, we identified at least four species-level phylogroups with differing functional potentials that affect how these bacteria interact with both their human host and other members of the human gut microbiome. Specifically, we identified and isolated Akkermansia strains that were able to synthesize vitamin B12. The ability to synthesize this important cofactor broadens the physiological capabilities of human-associated Akkermansia strains, fundamentally altering our understanding of how this important bacterial lineage may affect human health.

scholarly journals Bacterial associations in the healthy human gut microbiome across populations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mark Loftus ◽  
Sayf Al-Deen Hassouneh ◽  
Shibu Yooseph
Keyword(s):  
Gut Microbiome ◽  
Sequence Data ◽  
Bacterial Species ◽  
Human Populations ◽  
Human Gut ◽  
Healthy Human ◽  
Human Gut Microbiome ◽  
Genome Shotgun Sequence ◽  
Bacterial Associations ◽  
And Function

AbstractIn a microbial community, associations between constituent members play an important role in determining the overall structure and function of the community. The human gut microbiome is believed to play an integral role in host health and disease. To understand the nature of bacterial associations at the species level in healthy human gut microbiomes, we analyzed previously published collections of whole-genome shotgun sequence data, totaling over 1.6 Tbp, generated from 606 fecal samples obtained from four different healthy human populations. Using a Random Forest Classifier, we identified 202 signature bacterial species that were prevalent in these populations and whose relative abundances could be used to accurately distinguish between the populations. Bacterial association networks were constructed with these signature species using an approach based on the graphical lasso. Network analysis revealed conserved bacterial associations across populations and a dominance of positive associations over negative associations, with this dominance being driven by associations between species that are closely related either taxonomically or functionally. Bacterial species that form network modules, and species that constitute hubs and bottlenecks, were also identified. Functional analysis using protein families suggests that much of the taxonomic variation across human populations does not foment substantial functional or structural differences.

scholarly journals Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species

Cell ◽  
2015 ◽  
Vol 160 (4) ◽  
pp. 583-594 ◽  
Author(s):  
Sharon Greenblum ◽  
Rogan Carr ◽  
Elhanan Borenstein
Keyword(s):  
Copy Number Variation ◽  
Gut Microbiome ◽  
Copy Number ◽  
Strain Level ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Number Variation

scholarly journals HumGut: A comprehensive Human Gut prokaryotic genomes collection filtered by metagenome data

2020 ◽  
Author(s):  
Pranvera Hiseni ◽  
Knut Rudi ◽  
Robert C. Wilson ◽  
Finn Terje Hegge ◽  
Lars Snipen
Keyword(s):  
Gut Microbiome ◽  
Bacterial Species ◽  
Superior Performance ◽  
Human Gut ◽  
Taxonomic Assignment ◽  
Healthy Human ◽  
Human Gut Microbiome ◽  
Comprehensive Collection ◽  
Prokaryotic Genomes ◽  
Taxonomic Assignments

AbstractA major challenge with human gut microbiome studies is the lack of a publicly accessible human gut genome collection that is verifiably complete. We aimed to create Humgut, a comprehensive collection of healthy human gut prokaryotic genomes, to be used as a reference for worldwide human gut microbiome studies. We screened >2,300 healthy human gut metagenomes for the containment of >486,000 publicly available prokaryotic genomes. The contained genomes were then scored, ranked, and clustered based on their sequence identity, only to keep representative genomes per cluster, resulting thus in the creation of HumGut. Superior performance in the taxonomic assignment of metagenomic reads, classifying 97% of reads on average, is a benchmark advantage of HumGut. Re-analyses of healthy gut samples using HumGut revealed that >90% contained a core set of 129 bacterial species and that, on average, the guts of healthy people contain around 1,000 bacterial species. The HumGut collection will continuously be updated as the list of publicly available genomes and metagenomes expand. Our approach can also be extended to disease-associated genomes and metagenomes, in addition to other species. The comprehensive, yet slim HumGut database streamlines analyses while significantly improving taxonomic assignments in a field in dire need of method standardization and effectivity.

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