Gastro-intestinal and oral microbiome signatures associated with healthy aging

Study information

Needs review

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

31620923

DOI Digital object identifier for electronic documents.

10.1007/s11357-019-00098-8

URI Uniform resource identifier for web resources.

Authors

Singh H, Torralba MG, Moncera KJ, DiLello L, Petrini J, Nelson KE, Pieper R

Journal

GeroScience

Year

2019

The human oral and gut microbiomes influence health via competition for a distinct niche in the body with pathogens, via metabolic capabilities that increase host digestive capacity and generate compounds engaged in signaling pathways and modulation of immune system functions. Old age alters our metabolic and regenerative capacity. Following recruitment of 65 human subjects in the age range of 70 to 82, we discerned healthy aging (HA) and non-healthy aging (NHA) cohorts discordant in the occurrence of one or more major diseases: (1) cancer, (2) acute or chronic cardiovascular diseases, (3) acute or chronic pulmonary diseases, (4) diabetes, and (5) stroke or neurodegenerative disorders. We analyzed these cohorts' oral microbiomes (saliva) and gut microbiomes (stool) to assess diversity and identify microbial biomarkers for HA. In contrast to the gut microbiome where no change was observed, we found that the saliva microbiome had higher α-diversity in the HA compared with the NHA group. We observed the genus Akkermansia to be significantly more abundant in the gut microbiota of the HA group. Akkermansia muciniphila is a colonic mucin-degrading bacterium believed to have beneficial effects on gastrointestinal health, particularly in the context of diabetes and obesity. Erysipelotrichaceae UCG-003 was a taxon increased in abundance in the HA cohort. Streptococcus was the only genus observed to be significantly decreased in abundance in both the gut and oral microbiomes of the HA cohort compared with the NHA cohort. Our data support the notion that these microbes are potential probiotics to decrease the risks of non-healthy aging.

Experiment 1

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Curated date: 2021/01/10

Curator: WikiWorks

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Subjects

Location of subjects: United States of America

Host species Species from which microbiome was sampled (if applicable): Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: age age

Group 0 name Corresponds to the control (unexposed) group for case-control studies: healthy aging (HA)
Group 1 name Corresponds to the case (exposed) group for case-control studies: non-healthy aging (NHA)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: participants aged 70–82 who had a medical history linked to one or more of the following major disease categories: cancer, acute or chronic cardiovascular disease, acute or chronic pulmonary disease, chronic liver disease, diabetes and diabetic complications, and stroke or neurodegenerative disorder.
Group 0 sample size Number of subjects in the control (unexposed) group: 33
Group 1 sample size Number of subjects in the case (exposed) group: 32
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 6 weeks

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V1-V3

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Statistical test: DESeq2

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased
Chao1 Abundance-based estimator of species richness: decreased

Signature 1

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Curated date: 2021/01/10

Curator: Yu Wang

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Source: Figure 1a, Figure 2, Supplemental File S2

Description: Oral cavity microbiomes diversity and taxonomic differences between healthy aging (HA) and non-healthy aging (NHA) cohorts

Abundance in Group 1: increased abundance in non-healthy aging (NHA)

NCBI	Links
Streptococcus
Rothia
Veillonella

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Signature 2

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Your review change was submitted

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Curated date: 2021/01/10

Curator: Yu Wang

Revision editor(s): WikiWorks

Source: Figure 1a, Figure 2, Supplemental File S2

Description: Oral cavity microbiomes diversity and taxonomic differences between healthy aging (HA) and non-healthy aging (NHA) cohorts

Abundance in Group 1: decreased abundance in non-healthy aging (NHA)

NCBI	Links
Neisseria
Haemophilus
Fusobacterium
Capnocytophaga

Revision editor(s): WikiWorks

Experiment 2

Edit History Delete

Mark reviewed

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

Subjects

Location of subjects: United States of America

Host species Species from which microbiome was sampled (if applicable): Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: age age

Group 0 name Corresponds to the control (unexposed) group for case-control studies: healthy aging (HA)
Group 1 name Corresponds to the case (exposed) group for case-control studies: non-healthy aging (NHA)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: participants aged 70–82 who had a medical history linked to one or more of the following major disease categories: cancer, acute or chronic cardiovascular disease, acute or chronic pulmonary disease, chronic liver disease, diabetes and diabetic complications, and stroke or neurodegenerative disorder.
Group 0 sample size Number of subjects in the control (unexposed) group: 33
Group 1 sample size Number of subjects in the case (exposed) group: 32
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 6 weeks

Lab analysis

Sequencing type: 16S

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Statistical test: DESeq2

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged
Chao1 Abundance-based estimator of species richness: unchanged