Human Microbiome Journal最新文献

This study examined whether the diversity, composition and functional capacity of the saliva microbiota differed between children with low and high sedentary screen times. We analyzed the saliva microbiota using 16S rRNA (V3–V4) sequencing from 193 children with low and 183 children with high TV/screen viewing times while sitting. Microbiota diversity was higher among children with low screen times compared to children with high screen times. Furthermore, microbiota composition differed between the screen time groups. In addition, we identified ten differentially abundant taxonomic groups, including Veillonella, Prevotella and Streptococcus, and five differentially present metabolic pathways between the screen time groups. Children with high screen times exhibited a higher capacity to synthesize the fatigue- and activity-related amino acids ornithine and arginine. To conclude, children with high sedentary screen (sitting) times exhibited a lower diversity and a different composition and functionality of the microbiota compared to children with low screen times.

Cardiovascular disease (CVD) remains the leading cause of death globally, responsible for an estimated 17.9 million deaths annually. Traditional screening and diagnostic tests often fail to identify those at risk until a late stage, it is therefore essential to develop new predictive tests to enable diagnosis at an earlier stage to facilitate preventative treatments. Recently, many studies have shown that high levels of circulating Trimethylamine N-oxide (TMAO) are indicative of an increased risk of CVD. Through the analysis of TMAO levels it was found patients whose TMAO level was in the 4th quartile had a 2.29 fold increase of major adverse cardiac events (MACE) over patients whose level was in the 1st quartile (p < 0.05). These studies have also demonstrated the role of the gut microbiome in the formation of TMAO. This review will provide an overview of the role of the gut microbiome and explore the evidence linking TMAO and CVD.

Bacterial vaginosis (BV) is the most common vaginal problem in reproductive-age women. Recurrent BV, defined as having at least three BV episodes in one year, causes significant psychological distress and can prove challenging to resolve. Using 16S rRNA sequencing, we characterized the vaginal microbiome of 63 women aged 18–40 years. We compared the vaginal microbiome of 17 patients presenting with an acute episode of recurrent BV to 46 healthy controls. The effect of oral Metronidazole treatment on the vaginal microbiome of the recurrent BV patients was analyzed 7–10 days and 30–40 days after the completed the standard 7-day oral twice-a-day Metronidazole treatment regimen. Beta diversity (unweighted UniFrac distances) of recurrent BV patients’ vaginal microbiome differed significantly from healthy controls (p = 0.01). Compared to controls, Mycoplasma, Veillonella, and Sneathia genera were more dominant in the recurrent BV cohort, while Lactobacilleacae was less abundant. After one week of oral Metronidazole treatment, recurrent BV patients’ vaginal microbiome was significantly altered [alpha diversity, p = 0.005; beta diversity, p = 0.03], and there was an increase in healthy commensals such as Lactobacillaceae. However, these changes were not sustained one month after treatment. Our findings show that the vaginal microbiome of recurrent BV patients differs from healthy controls, and that Metronidazole as monotherapy may be insufficient treatment for recurrent BV, as it only alters the vaginal microbiome temporarily. Future investigations into alternative therapies that restore a healthy vaginal microbiome are necessary.

The cervicovaginal microbiome consists of community state types (CSTs) I-V. Several studies have reported positive correlations between health issues such as bacterial vaginosis (BV), acquisition of sexually transmitted infections (STIs), preterm labour and CST IV. The cervicovaginal microbiome in Afro-Caribbean women has never been characterized. Hence, this study aimed to determine the composition, CST, microbial function and resistome of the cervicovaginal microbiome in a cohort of Afro-Caribbean women using targeted (16S rRNA V4) and whole genome shotgun metagenomics. CST IV predominated in this ethnic group, with Prevotella (13.91 %) being the most abundant genus followed by Gardnerella (12.14 %). The relative abundance for Lactobacillus was 9.37 %. The most abundant species for Prevotella and Lactobacillus were P. timonensis (5.00 %) and L. iners (7.00 %), respectively. Taxa with significant nucleotide similarity to the less virulent culture collection strain G. vaginalis 409–05 (8.14 %) were more abundant than G. vaginalis ATCC 14019 (4.00 %) in this group that was asymptomatic of BV. Functional profiling revealed a high abundance of biological processes (such as flagellum-dependent cell motility, cell adhesion and quorum sensing) associated with biofilm activity. In the resistome, 2,753 predicted antimicrobial resistance (AMR) genes consisting of 28 types (mostly tet and Emr; relative abundance 52.94 % and 16.18 %, respectively) that can potentially confer resistance to tetracyclines and the macrolide-lincosamide streptogramin B group were identified. Theoretically, these AMR genes can impact the effectiveness of antibiotics commonly used in the treatment of STIs and BV. This study is the first to provide insight into the cervicovaginal microbiome and its resistome in Afro-Caribbean women.

The role of the human gut phageome (HGP) for a healthy gut microbiome is not well-established. This study aims to identify phages based on Reduced Metagenome Sequencing (RMS) fragments from an Indian mother and child cohort. For this study, fecal samples were collected from 17 mother-infant pairs at Nishanth Hospital, Tamil Nadu, India. RMS data analysis and shotgun sequencing approaches were used to assemble and identify the genome fragments. Out of the 156,926 RMS fragments, 434 were classified as bacteriophages by Kraken 2. Mapping of virus sequences in NCBI and de novo assembly with subsequent taxonomic assignment revealed 41 different phage species. The prevalence (>50%) of three bacteriophages was observed in mother and child; overall four phages were more prevalent in the mothers while one phage was more prevalent in the children. Even at the species level, mothers were found to have more diverse phage species than children. No significant association was observed for mother–child sharing of phages. This study highlights the prevalence of Caudovirales phages in healthy HGP and also the use of the RMS approach to study the phageome composition.

Vaginal microbiota has been postulated as a key contributor to the disproportionately higher HIV acquisition risk in women. The commensal bacterial communities in the vaginal tract have been implicated in HIV pathogenesis, with strict anaerobes such as Gardnerella and Prevotella causing inflammation and increased frequency of HIV target cells. Young African women are up to six times more likely to be infected with HIV than their male counterparts. The underlying biological mechanisms for increased susceptibility to HIV infection are not fully known, particularly among pregnant women who are also at risk of transmitting the infection to their unborn babies.

We characterized the vaginal microbiome of pregnant women receiving antenatal care. Using 16S rRNA sequencing, we analyzed the richness and abundances of the commensal bacterial communities within the female genital tract. Data was analyzed using qiime2 version 2018, Dada2 plugin, and Naive-Bayes classifier for Taxonomic assignment.

We report that 19% (35/179) of pregnant women had a Lactobacillus-dominant vaginal microbiota profile. Our findings show that the main cervicotypes (“CTs”) were CT1 which was predominantly non-iners Lactobacillus (6%, 11/179), CT2 which was dominated by L. iners (13%, 24/179), CT3 that was Gardnerella dominant (49%, 87/179) and CT4, a mixed CT co-dominated by L. iners, Gardnerella and Atopobium. Cervical lavage of women with non-Lactobacillus CT had significantly higher levels of inflammatory cytokines IL-1beta, TNF-alpha, and chemokines IL-6 and IL-8.

Highly diverse cervicotype (CT4) was associated with inflammation, a known catalyst of HIV acquisition and transmission, within pregnant women regardless of HIV sero-status.

Background

The oral microbiome is a complex assembly of microbial species, whose constituents can tilt the balance towards progression of oral disease or sustained health. Recently we identified sex-specific differences in the salivary microbiome contained within caries-active and caries-free children. In this study, we sought to ascertain if adjunctive dental therapies, including povidone iodine and chlorhexidine, were effective in shifting the cariogenic microbiome from dysbiosis to non-cariogenic health.

Design

We recruited young children (ages 2–12 years) to enter five enrollment groups, with each group (N = 9–30 participants/group) receiving caries restorative and/or adjunctive therapies, either singularly or in combination (OHSU IRB #6535). Saliva specimens were collected pre- and post-treatment (4–8 weeks) of caries preventive measures, and oral microbiota were identified using next generation sequencing (HOMINGS, Forsyth Institute, Cambridge, MA).

Results

With the use of multi-dimensional scaling plots, support vector machine learning, odds ratio analysis, and other statistical methods, we have determined that treatment with povidone iodine can shift the composition of the salivary cariogenic microbiome to include higher proportions of aerobic microorganisms, such as Stentrophomonas maltophila, as well as non-cariogenic, anaerobic microorganisms including Poryphyromonas and Fusobacterium species.

Conclusion

We have identified microorganisms that are associated with caries-active children and have determined that povidone iodine is an effective adjunctive therapy that has the potential to shift the composition of the cariogenic microbiome to one more closely aligned with non-cariogenic health.

The infection process of bacterial gastroenteritis often relies on the initial binding of toxins to carbohydrate receptors on host cells. We screened the human gut microbiota for microorganisms naturally expressing toxin-binding carbohydrate structures. Out of stool samples from four healthy adult donors, we isolated bacterial strains specifically binding the cholera toxin and the heat labile toxin. These results suggest a new mechanism by which the microbiome may shape people’s individual sensitivity to gastrointestinal infections. This study may also pave the way for the development of non-antibiotic microbiome based strategies to treat and prevent gastrointestinal infections.