The Distal Gut Bacterial Community of Some Primates and Carnivora

Abstract

Huge numbers of bacteria reside in the digestive tract of host and these microorganisms play a vital role in the host health, especially in the digestion of food and the development of immune system. Host phylogeny and diet, especially long-term diet, both have great influence on the gut bacterial community. Other aspects of host, such as gender, age, and the geography and weather they lived, are also correlated to their gut bacterial community. Feces are usually used for gut bacteria study and fecal bacteria can represent the distal gut bacteria. In order to determine the influence of the host phylogeny and diet on the composition of distal gut bacterial community and to interpret bacterial population and diversity in the intestinal of animals, the distal gut bacterial community of four kinds of primates and five kinds of carnivora (including herbivorous, omnivorous, and carnivorous) were investigated using high-throughput sequencing and the isolation of the Actinobacteria from fresh feces of several primates was processed. The results showed the host phylogeny had a greater influence on the distal gut bacterial community of the primates and carnivora than the host diet. A total of 44 bacteria phyla and two archaea phyla were detected, which indicated that the distal gut bacteria of these animals were abundant. The distal gut bacteria were relatively stable and wildly shared in primates and carnivora. The difference in distal gut bacteria of the two animal orders is mainly determined by relative abundance of most distal gut bacteria rather than by the taxa of these bacteria.

Vertebrate host phylogeny influences gut archaeal diversity

“…2a ). These findings suggest that host evolutionary history has a stronger effect on total archaeal community diversity among host species relative to diet (both general dietary categories and specific components), which corresponds with existing evidence of an association between archaeal diversity and host phylogeny 12 , 14 . However, these results contrast with our previous Bacteria-biased survey of the same sample data set, in which diet was an equal if not stronger explanatory variable relative to host phylogeny 13 .…”

Strong influence of vertebrate host phylogeny on gut archaeal diversity

“…Both host phylogeny and diet correlated with beta diversity, but host phylogeny was more consistently significant among diversity metrics and showed stronger correlations (Figure 2A). These findings suggest that host evolutionary history has a stronger effect on total archaeal community diversity among host species relative to diet (both general dietary categories and specific components), which corresponds with existing evidence of an association between archaeal diversity and host phylogeny (12, 14). Still, these results contrast our previous Bacteria-biased survey of the same sample dataset, in which diet was an equal if not stronger explanatory variable relative to host phylogeny (13).…”

“…While previous work has indicated that host phylogeny influences archaeal abundance (12–14, 30, 42), the work has largely been focused on methanogen diversity (especially Methanobrevibacter) and was strongly biased towards mammals. In this work, we not only identified a signal of host-Archaea phylosymbiosis while accounting for host diet, habitat, and other factors (Figure 2A), but we also identified specific archaeal ASVs to be associated with host phylogeny globally and for particular host clades (Figures 2C & S12), and we observed a significant signal of cophylogeny (Figure 2D & 2E).…”

“…Therefore, much likely remains unknown of archaeal diversity and community assembly in the vertebrate gut. Setting primer issues aside, previous studies have identified host evolutionary history and diet to be main factors influencing the gut microbiome (9)(10)(11)(12)(13) . While some studies have shown specific evidence that gut archaeal diversity is dictated by host relatedness (14)(15)(16)(17)(18) , focus has generally been on humans and certain mammalian clades.…”

First report on metagenomic analysis of gut microbiome in Island Flying Fox (Pteropus hypomelanus) revealing latitudinal correlation as opposed to host phylogeny in island populations of Malaysia

“…We focused on bacterial 16S rRNA gene of mitochondrial DNA (mtDNA) as the substitution rate is high, making this locus valuable for distinguishing organisms, especially among closely related species (Hillis & Dixon, 1991;Long & Dawid, 1980;Osorio, Collins, Romalde, & Toranzo, 2005). Further, metagenomic studies using 16S rRNA gene have been widely used to characterize gut microbial communities in wildlife such as bats, primates, tigers, and birds (Carrillo-Araujo et al, 2015;Chen et al, 2018;Garcia-Mazcorro et al, 2017;Philips et al, 2012). It has been shown that two variant regions in 16S rRNA gene, namely V3 and V4, provide sufficient phylogenetic information on bacteria (Huse et al, 2008;Liu, Lozupone, Hamady, Bushman, & Knight, 2007).…”