<p>Evaluation of gut bacterial community composition and antimicrobial resistome in pregnant and non-pregnant women from Saudi population</p>

Abstract

Background: Gut microbiota (GM) has recently been described as a functional reservoir of antimicrobial resistant genes (ARGs). However, the ARG-carrying bacterial species in the human gut has been poorly studied. This study, for the first time, is reporting bacterial communities' composition and antimicrobial resistome in the stool samples of pregnant and non-pregnant (NP) Saudi females. Methods: Gut bacterial community composition was analyzed by 16S amplicon sequencing and culturomics. High throughput MALDI-TOF technique was used for identification of the isolates from stool samples and evaluated for resistance against 13 antibiotics using the agar dilution method. Clinically important ARGs were PCR amplified from genomic DNA of the stool samples using gene-specific primers. Results: 16S amplicon sequencing revealed that GM of pregnant and NP women were predominantly comprised of phyla Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Bacterial diversity decreased in pregnant groups, whereas phylum Bacteroidetes declined significantly ( p <0.05) in the first trimester. We noticed a relatively high abundance of butyrate-producing bacteria (eg, Faecalibacterium spp. and Eubacterium spp.) in the gut of pregnant women, whereas Prevotella copri was found at significantly ( p <0.01) higher abundance in NP women. Moreover, about 14,694 isolates were identified and classified into 132 distinct species. The majority of the species belonged to phyla Firmicutes and Proteobacteria. About 8,125 isolates exhibited resistance against antibiotics. Out of 73 resistant-species, Enterococcus was the most diverse genus and Escherichia coli was the highly prevalent bacterium. The majority of the isolates were resistant to antibiotics; trimethoprim/sulfamethoxazole, cycloserine, and cefixime. ARGs encoding resistance against aminoglycoside, macrolide, quinolone, β-lactam, and tetracycline antibiotics were predominantly found in genomic DNA of the stool samples. Conclusion: We conclude that pregnancy-associated GM modulations may help to sustain a healthy pregnancy, but a higher proportion of antibiotic resistance could be deleterious for both maternal and fetal health.

16S amplicon sequencing of microbial communities in enriched and non-enriched sediments of non-volcanic hot spring with temperature gradients

“…Bacterial taxa retrieved in the culture-dependent method were not completely identified in 16S amplicon sequencing data. It is consistent with previous studies that showed partial overlapping in coverage of bacterial communities between the two methods ( Amrane et al, 2019 ; Khan et al, 2019 ; Lagier et al, 2012 ). Probably, 16S amplicon sequencing might miss the low abundant bacteria, and the specific culture media support the growth of low abundant species as previously noticed ( Diakite et al, 2019 ; Khan et al, 2019 ).…”

The immune system and microbiome in pregnancy

“…Although some studies did not observe any microbial changes over time during gestation [121], a consistent finding in most studies appears to be a reduced diversity in microbial composition [114,116,122,123]. This begs the question as to how this process is regulated.…”

Mobilome and Resistome Reconstruction from Genomes Belonging to Members of the Bifidobacterium Genus

“…Furthermore, different Escherichia coli strains presented in their genomes AR genes that counteracted carbapenem antibiotics [60,61], whereas bifidobacteria seemed to be very sensitive to this antibiotic class, and their genomes do not encompass any genes that could confer resistance toward this antibiotic. Notably, a recent study based on metagenomics analyses of the human gut microbiota revealed that Entrococcus and Enterobacter genera possessed a very high antibiotic resistance load [62]. These genera presented AR genes that could counteract different antibiotics, such as trimethoprim/sulfamethoxazole, metronizadole, cycloserine, and cefixime [62].…”

“…Notably, a recent study based on metagenomics analyses of the human gut microbiota revealed that Entrococcus and Enterobacter genera possessed a very high antibiotic resistance load [62]. These genera presented AR genes that could counteract different antibiotics, such as trimethoprim/sulfamethoxazole, metronizadole, cycloserine, and cefixime [62]. Moreover, different studies have demonstrated the presence of AR genes in the genomes of the members of Bacillus genus, used as probiotic bacteria in functional food and for animal feed [54,63].…”