Initial Sequencing and Characterization of the Gastrointestinal and Oral Microbiota in Urban Pakistani Adults

Abstract

We report the initial characterization of the gastrointestinal tract (gut) and oral microbiota (bacteria) in 32 urban Pakistani adults. Study participants were between ages 18 and 40, had body mass index between 18 and 25 Kg/m 2 , and were students or early-career professionals. These individuals donated a total of 61 samples (32 gut and 29 oral) that were subjected to 16S ribosomal RNA (rRNA) gene sequencing. Microbiome composition of Pakistani individuals was compared against the uBiome database of selected individuals who self-reported to be in excellent health. We observed strong gender-based differences in the gut microbiome of Pakistani individuals, a skewness toward Firmicutes, and unusually high levels of Proteobacteria in the Pakistani men. These observations may indicate microbiota dysbiosis, though 16S data alone can neither establish cause nor effect to human health. Albeit conducted on a smaller scale, our report provides a first snapshot about the composition and diversity of gut and oral microbiota communities in Pakistani individuals.

Characterization of the Gastrointestinal and Reproductive Tract Microbiota in Fertile and Infertile Pakistani Couples

“…Though, some authors have questioned the claim [ 63 ]. In our gut samples, Firmicutes dominated Bacteroidetes (mean relative abundance ranging from 53–63% vs. 11–23%, Table 1 ), which could indicate a tendency towards weight gain [ 40 ]. Firmicutes were significantly more abundant in fertile men vs. infertile men (63.32% vs. 53.45%, p = 0.03, two-tailed Mann–Whitney test) while Bacteroidetes were significantly more abundant in fertile women vs. infertile women (23.01% vs. 13.64%, p = 0.025, two-tailed Mann–Whitney test).…”

“…The gut microbiome also revealed fluctuations in key genera populations between fertile and infertile men and women. A notable appearance was of Succinivibrio population in infertile men (8.23% of total community), which are potentially sugar-metabolizing bacteria [ 67 ] and were previously detected in higher amounts in Pakistani men [ 40 ]. In turn, Succinivibrio was not amongst the top five genera in the gut microbiome of fertile men ( Table 2 ).…”

“…In cases where one of the partners was unavailable for sampling, only one partner was sampled. The study exclusion criteria included either the use of antibiotics or travel abroad in the last three months, women on menopause, and participants suffering from inflammatory bowel disease [ 40 ]. Both male (mean age 33.97 ± 6.14) and female (mean age 28.25 ± 5.47) participants belonged to the reproductive age (i.e., 19–45) years.…”

“…Each recruited study participant was instructed to provide two biological samples: (i) fecal sample, which was treated as the proxy for the gut microbiome, and (ii) the genital sample. Samples were self-collected by the study participants following the uBiome protocol for sampling (as also described in our previous study [ 40 ]). Participants were briefed about sampling instructions both in writing and in their native language.…”

Exploring the Ruminal Microbial Community Associated with Fat Deposition in Lambs

“…Based on the number of sequenced reads, we generated an OTU table by calculating the absolute abundance of each identified OTU for each sample. The data of OTU abundance were subsequently filtered, (Low count filter: At least 20% of its values should contain at least four counts [ 18 ]. Low variance filter: Percentage to remove 10% based on the Inter-quantile range [ 19 ]) and then transformed based on total sum scaling.…”