The Gut Microbiota of Healthy Chilean Subjects Reveals a High Abundance of the Phylum Verrucomicrobia

Abstract

The gut microbiota is currently recognized as an important factor regulating the homeostasis of the gastrointestinal tract and influencing the energetic metabolism of the host as well as its immune and central nervous systems. Determining the gut microbiota composition of healthy subjects is therefore necessary to establish a baseline allowing the detection of microbiota alterations in pathologic conditions. Accordingly, the aim of this study was to characterize the gut microbiota of healthy Chilean subjects using 16S rRNA gene sequencing. Fecal samples were collected from 41 young, asymptomatic, normal weight volunteers (age: 25 ± 4 years; ♀:48.8%; BMI: 22.5 ± 1.6 kg/m2) with low levels of plasma (IL6 and hsCRP) and colonic (fecal calprotectin) inflammatory markers. The V3-V4 region of the 16S rRNA gene of bacterial DNA was amplified and sequenced using MiSeq Illumina system. 109,180 ± 13,148 sequences/sample were obtained, with an α-diversity of 3.86 ± 0.37. The dominant phyla were Firmicutes (43.6 ± 9.2%) and Bacteroidetes (41.6 ± 13.1%), followed by Verrucomicrobia (8.5 ± 10.4%), Proteobacteria (2.8 ± 4.8%), Actinobacteria (1.8 ± 3.9%) and Euryarchaeota (1.4 ± 2.7%). The core microbiota representing the genera present in all the subjects included Bacteroides, Prevotella, Parabacteroides (phylum Bacteroidetes), Phascolarctobacterium, Faecalibacterium, Ruminococcus, Lachnospira, Oscillospira, Blautia, Dorea, Roseburia, Coprococcus, Clostridium, Streptococcus (phylum Firmicutes), Akkermansia (phylum Verrucomicrobia), and Collinsella (phylum Actinobacteria). Butyrate-producing genera including Faecalibacterium, Roseburia, Coprococcus, and Oscillospira were detected. The family Methanobacteriaceae was reported in 83% of the subjects and Desulfovibrio, the most representative sulfate-reducing genus, in 76%. The microbiota of the Chilean individuals significantly differed from those of Papua New Guinea and the Matses ethnic group and was closer to that of the Argentinians and sub-populations from the United States. Interestingly, the microbiota of the Chilean subjects stands out for its richness in Verrucomicrobia; the mucus-degrading bacterium Akkermansia muciniphila is the only identified member of this phylum. This is an important finding considering that this microorganism has been recently proposed as a hallmark of healthy gut due to its anti-inflammatory and immunostimulant properties and its ability to improve gut barrier function, insulin sensitivity and endotoxinemia. These results constitute an important baseline that will facilitate the characterization of dysbiosis in the main diseases affecting the Chilean population.

Comparative analysis of beneficial effects of Vancomycin treatment on Th1- and Th2-biased mice and role of gut microbiota

“…Lower expression of tight junction protein in vancomycin treated mice caused the increase in gut permeability resulting in the higher cecal index and fluid accumulation of cecal sample. It is reported that increased abundance of Verrucomicrobia causes a decrease in inflammation and enhances glucose metabolism of the host [77][78][79]. On the sixth day of vancomycin treatment, the current results revealed a decrease in Proteobacteria and increase in Verrucomicrobia which might have caused an anti-inflammatory effect in the gut.…”

“…It is well established that overexpression of Inflammatory cytokine like TNFα is associated with the higher gut permeability by suppressing the expression of tight junction proteins like occludin Page | 24 and claudin 1 [77,78]. Lower expression of tight junction protein in vancomycin treated mice caused the increase in gut permeability resulting in the higher cecal index and fluid accumulation of cecal sample.…”

The Gut Microbiome in Patients with Intestinal Failure: Current Evidence and Implications for Clinical Practice

“…14 Bacteria belonging to Firmicutes and Bacteroidetes phyla dominate the gut and, to a lesser extent, species from Verrucomicrobia, Proteobacteria, and Actinobacteria ( Figure 1). 15,16 The gut microbiome is important for several functions such as fermentation and absorption of nutrients in the colon, development of the immune system, and intestinal mucosal growth and integrity. 17,18 There is growing evidence that certain groups of bacteria such as Clostridia are important for normal intestinal function and protection against intestinal diseases, whereas other proinflammatory bacteria, specifically certain species belonging to Enterobacteriaceae, are harmful.…”

“…The gut microbiome becomes relatively stable in adulthood, with its intraindividual variation being lower than the differences seen between different subjects . Bacteria belonging to Firmicutes and Bacteroidetes phyla dominate the gut and, to a lesser extent, species from Verrucomicrobia, Proteobacteria, and Actinobacteria (Figure ) …”

Parasitic worm-derived ES-62 promotes health- and life-span in high calorie diet-fed mice

“…There was a striking loss of Verrucomicrobia, particularly in female mice (Figure 9a, lower panels), which exhibit unexpectedly high levels of these bacteria in the young (d56) control cohort and the d340 female chowfed group. Verrucomicrobia (primarily of the genus Akkermansia) are mucusdegrading commensals that have been reported to be a marker of gut health due to their ability to promote gut barrier integrity, Treg generation and insulin sensitivity 60,61 : thus, these findings may suggest, as with flies 45 , that female C57BL/6J mice may be particularly vulnerable to (HCD-induced) gut pathology during ageing. The failure of ES-62 to restore these commensals, and promote Treg responses in general 9 , may go some way to explaining why the helminth product does not extend lifespan in female HCD-fed mice but only in the male cohorts, which given their lower levels of Verrucomicrobia may be innately less susceptible to the pathological consequences of gut dysfunction.…”