Analyses of the Stability and Core Taxonomic Memberships of the Human Microbiome

Abstract

Analyses of the taxonomic diversity associated with the human microbiome continue to be an area of great importance. The study of the nature and extent of the commonly shared taxa (“core”), versus those less prevalent, establishes a baseline for comparing healthy and diseased groups by quantifying the variation among people, across body habitats and over time. The National Institutes of Health (NIH) sponsored Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine and better define what constitutes the taxonomic core within and across body habitats and individuals through pyrosequencing-based profiling of 16S rRNA gene sequences from oral, skin, distal gut (stool), and vaginal body habitats from over 200 healthy individuals. A two-parameter model is introduced to quantitatively identify the core taxonomic members of each body habitat’s microbiota across the healthy cohort. Using only cutoffs for taxonomic ubiquity and abundance, core taxonomic members were identified for each of the 18 body habitats and also for the 4 higher-level body regions. Although many microbes were shared at low abundance, they exhibited a relatively continuous spread in both their abundance and ubiquity, as opposed to a more discretized separation. The numbers of core taxa members in the body regions are comparatively small and stable, reflecting the relatively high, but conserved, interpersonal variability within the cohort. Core sizes increased across the body regions in the order of: vagina, skin, stool, and oral cavity. A number of “minor” oral taxonomic core were also identified by their majority presence across the cohort, but with relatively low and stable abundances. A method for quantifying the difference between two cohorts was introduced and applied to samples collected on a second visit, revealing that over time, the oral, skin, and stool body regions tended to be more transient in their taxonomic structure than the vaginal body region.

Evidence for rapid, tide-related shifts in the microbiome of the coral Coelastrea aspera

“…Although the significance of the 'core' microbiome of corals and its relationship with more 'transient' members of the holobiont remains to be fully understood, there are striking parallels between the results of this study and those found in other systems (Shade and Handelsman 2012;Li et al 2013;Dirksen et al 2016). These consistencies may have particular relevance to the link between the stability of the microbiome and its role in overall health status.…”

Profiles and technological requirements of urogenital probiotics

“…Hansen, Denmark; minimum 2.56 x 10 9 colony forming units (CFU) of each strain), included in vaginal capsules Double blinded, placebo-controlled crossover study, in fourteen post-menopausal women (natural menopause) with an intermediate Nugent Score (4)(5)(6). Administration of probiotic vaginal capsules or placebo twice a day for 3 days.…”

“…In the vaginal microbiome, lactobacilli constitute the dominant proportion (80%) of bacteria inhabiting the healthy women's vagina [1,2,[5][6][7]12,13]. Some LAB strains have found to be endogenous from healthy human vagina, where there is a rather stable microbiota [14][15][16].…”

“…The microbiome colonizing the human body provides the host a huge coding and metabolic activities as will be described later [1,2,[5][6][7][8]. Among this microbiota there are health-promoting indigenous species that are commonly consumed as live supplements [9].…”

“…Their genomes have sizes varying from 1.8 to 3.3 MB, and their G+C content range from 33 to 51%. In such a way, a Lactobacillus core genome has been described, constituted by 383 sets of orthologous genes, designed as Lactobacillus core genome [5,10,11].…”