A multi-omic cohort as a reference point for promoting a healthy human gut microbiome

Abstract

1 More than a decade of gut microbiome studies have a common goal for human 2 health. As most of the disease studies sample the elderly or the middle-aged, a 3 reference cohort for young individuals has been lacking. It is also not clear what 4 other omics data need to be measured to better understand the gut microbiome.5 Here we present high-depth metagenomic shotgun sequencing data for the fecal 6 microbiome together with other omics data in a cohort of 2,183 adults, and observe 7 a number of vitamins, hormones, amino acids and trace elements to correlate with 8 the gut microbiome and cluster with T cell receptors. Associations with physical 9 fitness, sleeping habits and dairy consumption are identified in this large multi-omic 1 0 cohort. Many of the associations are validated in an additional cohort of 1,404 1 1 individuals. Our comprehensive data are poised to advise future study designs to 1 2 better understand and manage our gut microbiome both in population and in 1 3 mechanistic investigations.

The vagino-cervical microbiome as a woman’s life history

“…L. iners and other Lactobacilli have been detected in the placenta (Aagaard et al, 2014; de Goffau et al, 2019; Lannon et al, 2019; Macklaim et al, 2011; Seferovic et al, 2019), amniotic fluid, nasal and pharyngeal sites (Boeck et al; Wang et al, 2018a). Aldosterone, a major mineralocorticoid for which we observe association with potentially beneficial bacteria in the gut microbiome in an accompanying study (Jie et al, 2019), positively associated with L. crispatus in the vagino-cervical microbiome, while a precursor for aldosterone, corticosterone, positively associated with L. iners (Figure 7). How vitamin D and hormone metabolism might impact the vagino-cervical microbiome would require further studies.…”

“…7). The plasma metabolites and T cell receptor types associated with the vagino-cervical microbiome are distinct from those associated with the fecal microbiome (Jie et al, 2019). Vaginal Prevotella could induce more CD4+ T cells (Gosmann et al, 2017), but the Prevotella species are not the dominant gut species of Prevotella copri which may compete with Bacteroides spp.…”

“…The vagino-cervical microbiome also better predicted facial skin features compared to the fecal microbiome (Jie et al, 2019), perhaps due to a clearer pattern of hormone and immune signatures. The associations with physical fitness tests and self-reported physical activities were however less prominent in the vagino-cervical compared to the fecal microbiome (Jie et al, 2019), as the changes due to pregnancy, delivery and breastfeeding may not be easily modifiable with physical activity. As a densely populated microbiota other than the distal gut, the vagino-cervical microbiota has the potential to reflect or even influence physiology elsewhere in the human body.…”

Over 50000 metagenomically assembled draft genomes for the human oral microbiome reveal new taxa

“…In order to substantially increase the amount of oral microbiome data, we shotgun sequenced 2284 saliva and 391 tongue dorsum samples from the 4D-SZ cohort 3, 12, 22 , 671 saliva samples from five ethnic groups of Yunnan province, producing over 43.19 terabytes of sequence data ( Supplementary Table 1 ). Together with 808 published samples from 5 studies 6, 23–26 that have not been used for metagenomic assembly ( Supplementary Table 1 ), a total of 4,154 oral samples with metagenomic data were obtained.…”

“…The human microbiome has been implicated in a growing number of diseases. The majority of microbial cells is believed to reside in the large intestine 1 and cohorts with fecal metagenomic data contain over 1000 individuals 2, 3 . For the oral microbiome, hundreds of metagenomic shotgun-sequenced samples have been available from the Human Microbiome Project (HMP) and for rheumatoid arthritis 4–6 .…”