Deep insights into the gut microbial community of extreme longevity in south Chinese centenarians by ultra-deep metagenomics and large-scale culturomics

Abstract

The gut microbes play important roles in human longevity and the gut microbiota profile of centenarians shows some unique features from young adults. Nowadays, most microbial studies on longevity are commonly based on metagenomic sequencing which may lose information about the functional microbes with extremely low abundance. Here, we combined in-depth metagenomic sequencing and large-scale culturomics to reveal the unique gut microbial structure of a Chinese longevity population, and to explore the possible relationship between intestinal microbes and longevity. Twenty-five healthy Hainan natives were enrolled in the study, including 12 centenarians and 13 senior neighbors. An average of 51.1 Gb raw sequencing data were obtained from individual fecal sample. We assembled 1778 non-redundant metagenomic assembled genomes (MAGs), 33.46% of which cannot be classified into known species. Comparison with the ordinary people in Hainan province, the longevous cohort displayed significantly decreased abundance of butyrate-producing bacteria and largely increased proportion of Escherichia coli, Desulfovibrio piger and Methanobrevibacter smithii. These species showed a constant change with aging. We also isolated 8,030 strains from these samples by large-scale culturomics, most of which belonged to 203 known species as identified by MALDI-TOF. Surprisingly, only 42.17% of the isolated species were also detected by metagenomics, indicating obvious complementarity between these two approaches. Combination of two complement methods, in-depth metagenomic sequencing and culturomics, provides deeper insights into the longevity-related gut microbiota. The uniquely enriched gut microbes in Hainan extreme decades population may help to promote health and longevity.

Age-Related Dynamics of Methanogenic Archaea in the Human Gut Microbiome: Implications for Longevity and Health

“…1B, Supplementary Fig. 3C), as observed previously (6). With respect to the bacteriome, we could observe that at phylum level, Firmicutes, Proteobacteria, Actinobacteriota, and Bacteroidota were the dominant bacterial taxa in each age group, which was in accordance with previous reports with different cohorts (Fig.…”

“…We then delved more into the differences of the archaeal profile of different age groups. The increased relative abundance of M. smithii with advancement of age, and the possible increased abundance of this methanogen prior to longevity has been previously reported (62). Our study however provided evidence that although there is a steady increase in relative abundance of Methanobacteria with the progression of age, there is a transition phase where the OAs are characterized by the increased abundance of Ca.…”

Gut microbiota as an antioxidant system in centenarians associated with high antioxidant activities of gut-resident Lactobacillus

“…Consistent with previous findings, age-related significantly increased abundances of Methanobrevibacter , methanogenic genes, and microbial diversity may be associated with prolonged colonic transit time, which was observed in older adults 47 , 48 . Methanobrevibacter is gradually enriched with age, which may have a role in longevity 49 .…”

Intestinal microbiome in normal ageing, frailty and cognition decline

“…The microbiome of centenarians, as models of longevity and successful ageing, has been particularly studied. It is characterized by depletion of taxa with purported health-promoting activity, including synthesis of short-chain fatty acids (SCFAs), fundamental anti-inflammatory and pro-anabolic mediators [5][6][7][8]. However, one study conducted in Chinese centenarians and their offspring suggested that metabolic capacity of synthetizing SCFAs was maintained, at the functional level, in extreme ages [8].…”

“…However, one study conducted in Chinese centenarians and their offspring suggested that metabolic capacity of synthetizing SCFAs was maintained, at the functional level, in extreme ages [8]. The microbiome of centenarians was also characterized by high biodiversity, increased representation of Prevotella at the expense of Bacteroides, and high abundance of 'core taxa' such as Bifidobacteria and Methanobrevibacter in comparison with younger people [5][6][7][8].…”