Gastro-intestinal and oral microbiome signatures associated with healthy aging

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2023-4-16

study design

prospective cohort

Citation

PMID PubMed identifier for scientific articles.

31620923

DOI Digital object identifier for electronic documents.

10.1007/s11357-019-00098-8

URI

Authors

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

Journal

GeroScience

Year

2019

Keywords:

16S rRNA, Akkermansia, Chronic disease, Gut microbiome, Healthy aging, Longevity, Metagenomic analysis, Oral microbiome, Streptococcus

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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Reviewed Marked as Reviewed by Claregrieve1 on 2023-4-16

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Claregrieve1

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

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).

centered log-ratio

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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Reviewed Marked as Reviewed by Claregrieve1 on 2023-4-16

Curated date: 2021/01/10

Curator: Yu Wang

Revision editor(s): WikiWorks, Claregrieve1

Source: 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	Quality Control	Links
Rothia
Streptococcus
Veillonella
Lactobacillus
Bifidobacterium

Revision editor(s): WikiWorks, Claregrieve1

Signature 2

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Reviewed Marked as Reviewed by Claregrieve1 on 2023-4-16

Curated date: 2021/01/10

Curator: Yu Wang

Revision editor(s): WikiWorks, Claregrieve1

Source: 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	Quality Control	Links
Capnocytophaga
Fusobacterium
Haemophilus
Neisseria
Tannerella
Treponema
Eikenella
Lautropia
Johnsonella
Cardiobacterium
Comamonas
Filifactor
Fusobacterium sp.
Propionibacterium
Haemophilus sp.
Corynebacterium
Porphyromonas
Peptoclostridium
candidate division SR1 bacterium

Revision editor(s): WikiWorks, Claregrieve1

Experiment 2

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Curated date: 2021/01/10

Curator: WikiWorks

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Differences from previous experiment shown

Subjects

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

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: Not specified

Alpha Diversity

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