A Scoping Review Evaluating the Current State of Gut Microbiota Research in Africa

Getting ahead of human-associated microbial decline in Africa: the urgency of sampling in light of epidemiological transition

Evidence is growing that human-associated early-life microbial diversity modulates health over the long term, via effects in the infant termed 'immune and metabolic education'. Documenting high microbial diversity contexts, such as in Africa, thus, has rich potential for understanding this aspect of the landscape of health. Yet, change on the continent is occurring rapidly, and microbial communities are shifting as behaviors and diets are altered, and antibiotic use expands; we may be losing the opportunity to obtain relevant data. After introducing what is known about the effects of early life microbial diversity on late life health, we provide an overview of what is known of the current, and expected future, trajectory of human-associated microbial diversity in Africa, introducing data on the core drivers. We argue that critical insights may be lost if better understanding of infant microbial communities in Africa is not obtained soon.

Characterization of the intestinal microbiota in MSM with HIV infection

BACKGROUND

HIV-infected persons demonstrate notable disturbances in their intestinal microbiota; however, the impact of intestinal microbiota on HIV susceptibility in men who have sex with men (MSM), as well as the effects of HIV and antiretroviral therapy (ART) on their gut microbiota, remains under active study. Thus, our research focuses on clarifying the distinctions in intestinal microbiota composition among uninfected MSM and non-MSM healthy controls, investigating the alterations in early-stage intestinal microbial communities following HIV infection, and assessing how ART affects the intestinal microbiota.

METHODS

This study enrolled four participant groups: uninfected MSM, Recent HIV-1 infection (RHI) MSM, MSM on ART, and non-MSM healthy controls, with 30 individuals in each group. We utilized 16S ribosomal DNA (16S rDNA) amplicon sequencing to analyze fecal microbiota and employed Luminex multiplex assays to measure plasma markers for microbial translocation (LBP, sCD14) and the inflammatory marker CRP.

FINDINGS

Comparing uninfected MSM to non-MSM healthy controls, no substantial variances were observed in α and β diversity. Uninfected MSM had higher average relative abundances of Bacteroidetes, Prevotella, and Alloprevotella, while Bacteroides, Firmicutes, and Faecalibacterium had lower average relative abundances. MSM on ART had lower intestinal microbiota diversity than RHI MSM and uninfected MSM. In MSM on ART, Megasphaera and Fusobacterium increased, while Faecalibacterium and Roseburia decreased at genus level. Additionally, treatment with a non-nucleoside reverse transcriptase inhibitor (NNRTI) led to significant alterations in intestinal microbiota diversity and composition compared to RHI MSM. The random forest model showed that HIV infection biomarkers effectively distinguished between newly diagnosed HIV-infected MSM and HIV-negative MSM, with an ROC AUC of 76.24% (95% CI: 61.17-91.31%).

CONCLUSIONS

MSM showed early intestinal microbiota imbalances after new HIV infection. MSM on ART experienced worsened dysbiosis, indicating a combined effect of HIV and ART. NNRTI-based treatment notably changed intestinal microbiota, suggesting a potential direct impact of NNRTI drugs on intestinal microbiota.

COVID-19 influenced gut dysbiosis, post-acute sequelae, immune regulation, and therapeutic regimens

The novel coronavirus disease 2019 (COVID-19) pandemic outbreak caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has garnered unprecedented global attention. It caused over 2.47 million deaths through various syndromes such as acute respiratory distress, hypercoagulability, and multiple organ failure. The viral invasion proceeds through the ACE2 receptor, expressed in multiple cell types, and in some patients caused serious damage to tissues, organs, immune cells, and the microbes that colonize the gastrointestinal tract (GIT). Some patients who survived the SARS-CoV-2 infection have developed months of persistent long-COVID-19 symptoms or post-acute sequelae of COVID-19 (PASC). Diagnosis of these patients has revealed multiple biological effects, none of which are mutually exclusive. However, the severity of COVID-19 also depends on numerous comorbidities such as obesity, age, diabetes, and hypertension and care must be taken with respect to other multiple morbidities, such as host immunity. Gut microbiota in relation to SARS-CoV-2 immunopathology is considered to evolve COVID-19 progression via mechanisms of biochemical metabolism, exacerbation of inflammation, intestinal mucosal secretion, cytokine storm, and immunity regulation. Therefore, modulation of gut microbiome equilibrium through food supplements and probiotics remains a hot topic of current research and debate. In this review, we discuss the biological complications of the physio-pathological effects of COVID-19 infection, GIT immune response, and therapeutic pharmacological strategies. We also summarize the therapeutic targets of probiotics, their limitations, and the efficacy of preclinical and clinical drugs to effectively inhibit the spread of SARS-CoV-2.

Transmission and Persistence of Infant Gut-Associated Bifidobacteria

Bifidobacterium infantis are the primary colonizers of the infant gut, yet scientific research addressing the transmission of the genus Bifidobacterium to infants remains incomplete. This review examines microbial reservoirs of infant-type Bifidobacterium that potentially contribute to infant gut colonization. Accordingly, strain inheritance from mother to infant via the fecal-oral route is likely contingent on the bifidobacterial strain and phenotype, whereas transmission via the vaginal microbiota may be restricted to Bifidobacterium breve. Additional reservoirs include breastmilk, horizontal transfer from the environment, and potentially in utero transfer. Given that diet is a strong predictor of Bifidobacterium colonization in early life and the absence of Bifidobacterium is observed regardless of breastfeeding, it is likely that additional factors are responsible for bifidobacterial colonization early in life.