The infant microbiome plays an essential role in human health and its assembly is determined by maternal– offspring exchanges of microbiota. This process is affected by several practices, including Cesarean section (C-section), perinatal antibiotics, and formula feeding, that have been linked to increased risks of metabolic and immune diseases. Here we review recent knowledge about the impacts on infant microbiome assembly, discuss preventive and restorative strategies to ameliorate the effects of these impacts, and highlight where research is needed to advance this field and improve the health of future generations.

Summary Background Little data are available regarding the effectiveness and associated microbiome changes of faecal microbiota transplantation (FMT) for Clostridium difficile infection (CDI) in children, especially in those with inflammatory bowel disease (IBD) with presumed underlying dysbiosis. Aim To investigate C. difficile eradication and microbiome changes with FMT in children with and without IBD. Methods Children with a history of recurrent CDI (≥3 recurrences) underwent FMT via colonoscopy. Stool samples were collected pre‐FMT and post‐FMT at 2–10 weeks, 10–20 weeks and 6 months. The v4 hypervariable region of the 16S rRNA gene was sequenced. C. difficile toxin B gene polymerase chain reaction was performed. Results Eight children underwent FMT for CDI; five had IBD. All had resolution of CDI symptoms. All tested had eradication of C. difficile at 10–20 weeks and 6 months post‐FMT. Pre‐FMT patient samples had significantly decreased bacterial richness compared with donors (P = 0.01), in those with IBD (P = 0.02) and without IBD (P = 0.01). Post‐FMT, bacterial diversity in patients increased. Six months post‐FMT, there was no significant difference between bacterial diversity of donors and patients without IBD; however, bacterial diversity in those with IBD returned to pre‐FMT baseline. Microbiome composition at 6 months in IBD‐negative patients more closely approximated donor composition compared to IBD‐positive patients. Conclusions FMT gives sustained C. difficile eradication in children with and without IBD. FMT‐restored diversity is sustained in children without IBD. In those with IBD, bacterial diversity returns to pre‐FMT baseline by 6 months, suggesting IBD host‐related mechanisms modify faecal microbiome diversity.

BackgroundConventional diagnosis of malaria has relied upon either clinical diagnosis or microscopic examination of peripheral blood smears. These methods, if not carried out exactly, easily result in the over- or under-diagnosis of malaria. The reliability and accuracy of malaria RDTs, even in extremely challenging health care settings, have made them a staple in malaria control programmes. Using the setting of a pilot introduction of malaria RDTs in Greater Garissa, North Eastern Province, Kenya, this study aims to identify and understand perceptions regarding malaria diagnosis, with a particular focus on RDTs, and treatment among community members and health care workers (HCWs).MethodsThe study was conducted in five districts of Garissa County. Focus group discussions (FGD) were performed with community members that were recruited from health facilities (HFs) supported by the MENTOR Initiative. In-depth interviews (IDIs) and FGDs with HCWs were also carried out. Interview transcripts were then coded and analysed for major themes. Two researchers reviewed all codes, first separately and then together, discussed the specific categories, and finally characterized, described, and agreed upon major important themes.ResultsThirty-four FGDs were carried out with a range of two to eight participants (median of four). Of 157 community members, 103 (65.6%) were women. The majority of participants were illiterate and the highest level of education was secondary school. Some 76% of participants were of Somali ethnicity. Whilst community members and HCWs demonstrated knowledge of aspects of malaria transmission, prevention, diagnosis, and treatment, gaps and misconceptions were identified. Poor adherence to negative RDT results, unfamiliarity and distrust of RDTs, and an inconsistent RDT supply were the main challenges to become apparent in FGDs and IDIs.ConclusionGaps in knowledge or incorrect beliefs exist in Greater Garissa and have the potential to act as barriers to complete and correct malaria case management. Addressing these knowledge gaps requires comprehensive education campaigns and a reliable and constant RDT supply. The results of this study highlight education and supply chain as key factors to be addressed in order to make large scale roll out of RDTs as successful and effective as possible.

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Fecal microbiota transplantation (FMT) has rapidly grown in notoriety and popularity worldwide as a treatment for both recurrent and refractory C. difficile infection (CDI), as well as for a myriad of other indications, with varying levels of evidence to justify its use. At present, FMT use in the U.S. has not received marketing approval from the U.S. Food and Drug Administration (FDA), but is permitted under “enforcement discretion” for CDI not responding to standard therapy. Meanwhile, the rising interest in the gut microbiome throughout mainstream media has paved the way for “do-it-yourself” (DIY) adaptations of the procedure. This access and unregulated use, often outside any clinical supervision, has quickly outpaced the medical community’s research and regulatory efforts. While some studies have been able to demonstrate the success of FMT in treating conditions other than CDI—studies on ulcerative colitis have been particularly promising—little is still known about the treatmen’s mechanism of action or long-term side effects. Likewise, screening of donor stool is in its early stages in terms of protocol standardization. In this paper, we explore the regulatory and ethical concerns that arise from the need to balance access to a nascent but promising innovative treatment with the need for research into its efficacy, risk profile, and long-term impact.