Metabolic independence drives gut microbial colonization and resilience in health and disease

Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge. Here we use...

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Published inGenome Biology Vol. 24; no. 1; p. 78
Main Authors Watson, Andrea R., Füssel, Jessika, Veseli, Iva, DeLongchamp, Johanna Zaal, Silva, Marisela, Trigodet, Florian, Lolans, Karen, Shaiber, Alon, Fogarty, Emily, Runde, Joseph M., Quince, Christopher, Yu, Michael K., Söylev, Arda, Morrison, Hilary G., Lee, Sonny T. M., Kao, Dina, Rubin, David T., Jabri, Bana, Louie, Thomas, Eren, A. Murat
Format Journal Article
LanguageEnglish
Published England BioMed Central 17.04.2023
BMC
Subjects
Amino Acids
biosynthesis
Community composition
community structure
Digestive system
Disease
Dysbacteriosis
Ecology
environmental factors
Fecal Microbiota Transplantation
Fecal microflora
Feces
Gastrointestinal Microbiome
genome
Genomes
Human gut microbiome
human health
Humans
Inflammation
Inflammatory bowel disease
Intestinal microflora
intestinal microorganisms
Metabolic independence
Metabolism
metabolites
Metagenomics
Microbial colonization
microbial communities
Microbial metabolism
microbiome
Microbiomes
Microbiota
Nucleotides
Success
surveys
Taxonomy
Transplantation
Transplants & implants
Vitamins
Microbial colonization
Human gut microbiome
Metabolic independence
Fecal microbiota transplantation
Microbial metabolism
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Abstract Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge. Here we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients. These observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments and reveal taxon-independent markers of "dysbiosis" that may explain why widespread yet typically low-abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.
AbstractList Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge. Here we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients. These observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments and reveal taxon-independent markers of "dysbiosis" that may explain why widespread yet typically low-abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.
BackgroundChanges in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge.ResultsHere we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients.ConclusionsThese observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments and reveal taxon-independent markers of “dysbiosis” that may explain why widespread yet typically low-abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.
Abstract Background Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge. Results Here we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients. Conclusions These observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments and reveal taxon-independent markers of “dysbiosis” that may explain why widespread yet typically low-abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.
Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge.BACKGROUNDChanges in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge.Here we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients.RESULTSHere we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients.These observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments and reveal taxon-independent markers of "dysbiosis" that may explain why widespread yet typically low-abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.CONCLUSIONSThese observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments and reveal taxon-independent markers of "dysbiosis" that may explain why widespread yet typically low-abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.
BACKGROUND: Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge. RESULTS: Here we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients. CONCLUSIONS: These observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments and reveal taxon-independent markers of “dysbiosis” that may explain why widespread yet typically low-abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.
ArticleNumber 78
Author DeLongchamp, Johanna Zaal
Quince, Christopher
Fogarty, Emily
Shaiber, Alon
Rubin, David T.
Trigodet, Florian
Jabri, Bana
Lee, Sonny T. M.
Veseli, Iva
Watson, Andrea R.
Runde, Joseph M.
Yu, Michael K.
Kao, Dina
Morrison, Hilary G.
Silva, Marisela
Lolans, Karen
Söylev, Arda
Eren, A. Murat
Louie, Thomas
Füssel, Jessika
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/37069665$$D View this record in MEDLINE/PubMed
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Issue 1
Keywords Microbial colonization
Human gut microbiome
Metabolic independence
Fecal microbiota transplantation
Microbial metabolism
Language English
License 2023. The Author(s).
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ssj0017866
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Snippet Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome....
BackgroundChanges in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut...
BACKGROUND: Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut...
Abstract Background Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human...
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SubjectTerms Amino Acids
biosynthesis
Community composition
community structure
Digestive system
Disease
Dysbacteriosis
Ecology
environmental factors
Fecal Microbiota Transplantation
Fecal microflora
Feces
Gastrointestinal Microbiome
genome
Genomes
Human gut microbiome
human health
Humans
Inflammation
Inflammatory bowel disease
Intestinal microflora
intestinal microorganisms
Metabolic independence
Metabolism
metabolites
Metagenomics
Microbial colonization
microbial communities
Microbial metabolism
microbiome
Microbiomes
Microbiota
Nucleotides
Success
surveys
Taxonomy
Transplantation
Transplants & implants
Vitamins
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Title Metabolic independence drives gut microbial colonization and resilience in health and disease
URI https://www.ncbi.nlm.nih.gov/pubmed/37069665
https://www.proquest.com/docview/2803038385
https://www.proquest.com/docview/2802885675
https://www.proquest.com/docview/3153170571
https://pubmed.ncbi.nlm.nih.gov/PMC10108530
https://doaj.org/article/44bec04531e04bb28a130bfd182cd4c1
Volume 24
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