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Microbial colonization of the neonatal gut involves maternal seeding, which is partially disrupted in cesarean-born infants and after intrapartum antibiotic prophylaxis. However, other physically close individuals could complement such seeding. To assess the role of both parents and of induced seeding, we analyzed two longitudinal metagenomic datasets (health and early life microbiota [HELMi]: N = 74 infants, 398 samples, and SECFLOR: N = 7 infants, 35 samples) with cesarean-born infants who received maternal fecal microbiota transplantation (FMT). We found that the father constitutes a stable source of strains for the infant independently of the delivery mode, with the cumulative contribution becoming comparable to that of the mother after 1 year. Maternal FMT increased mother-infant strain sharing in cesarean-born infants, raising the average bacterial empirical growth rate while reducing pathogen colonization. Overall, our results indicate that maternal seeding is partly complemented by that of the father and support the potential of induced seeding to restore potential deviations in this process., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

The composition and maturation of the early-life microbiota are modulated by a number of perinatal factors, whose interplay in relation to microbial vertical transmission remains inadequately elucidated. Using recent strain-tracking methodologies, we analyzed mother-to-infant microbiota transmission in two different birth environments: hospital-born (vaginal/cesarean) and home-born (vaginal) infants and their mothers. While delivery mode primarily explains initial compositional differences, place of birth impacts transmission timing-being early in homebirths and delayed in cesarean deliveries. Transmission patterns vary greatly across species and birth groups, yet certain species, like Bifidobacterium longum, are consistently vertically transmitted regardless of delivery setting. Strain-level analysis of B. longum highlights relevant and consistent subspecies replacement patterns mainly explained by breastfeeding practices, which drive changes in human milk oligosaccharide (HMO) degrading capabilities. Our findings highlight how delivery setting, breastfeeding duration, and other lifestyle preferences collectively shape vertical transmission, impacting infant gut colonization during early life., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

The Segatella copri (formerly Prevotella copri) complex (ScC) comprises taxa that are key members of the human gut microbiome. It was previously described to contain four distinct phylogenetic clades. Combining targeted isolation with large-scale metagenomic analysis, we defined 13 distinct Segatella copri-related species, expanding the ScC complex beyond four clades. Complete genome reconstruction of thirteen strains from seven species unveiled the presence of genetically diverse large circular extrachromosomal elements. These elements are consistently present in most ScC species, contributing to intra- and inter-species diversities. The nine species-level clades present in humans display striking differences in prevalence and intra-species genetic makeup across human populations. Based on a meta-analysis, we found reproducible associations between members of ScC and the male sex and positive correlations with lower visceral fat and favorable markers of cardiometabolic health. Our work uncovers genomic diversity within ScC, facilitating a better characterization of the human microbiome., Competing Interests: Declaration of interests T.D.S. and J.W. are co-founders of ZOE Ltd. (ZOE). S.E.B. and T.D.S. receive payments as consultants to ZOE. R.D. is employed by ZOE. J.W., R.D., S.E.B., and T.D.S. receive options in ZOE., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)

Fecal microbiota transplantation (FMT) has achieved satisfactory results in preventing the recurrence of Clostridioides difficile infection, but these positive outcomes have only been partially replicated in other diseases. Several factors influence FMT success, including those related to donors and recipients (including diversity and specific composition of the gut microbiome, immune system, and host genetics) as well as to working protocols (fecal amount and number of infusions, route of delivery, and adjuvant treatments). Moreover, initial evidence suggests that the clinical success of FMT may be related to the degree of donor microbial engraftment. The application of cutting-edge technologies for microbiome assessment, along with changes in the current vision of fecal transplants, are expected to improve FMT protocols and outcomes. Here, we review the key determinants of FMT success and insights and strategies that will enable a close integration of lab-based and clinical approaches for increasing FMT success., Competing Interests: Declaration of interests A.G. reports personal fees for consultancy for Eisai S.r.l., 3PSolutions, Real Time Meeting, Fondazione Istituto Danone, Sinergie S.r.l. Board MRGE, and SanofiS.p.A; personal fees for acting as a speaker for Takeda S.p.A, AbbVie, and Sandoz S.p.A; and personal fees for acting on advisory boards for VSL3 and Eisai. G.C. has received personal fees for acting as an advisor for Ferring Therapeutics. H.S. reports lecture fees, board membership, or consultancy from Amgen, Fresenius, IPSEN, Actial, Astellas, Danone, THAC, biose, BiomX, Eligo, Immusmol, Adare, Nestle, Ferring, MSD, Bledina, Pfizer, Biocodex, BMS, Bromatech, Gilead, Janssen, Mayoli, Roche, Sanofi, Servier, Takeda, Abbvie, has stocks from Enterome bioscience, and is co-founder of Exeliom Biosciences. G.I. has received personal fees for acting as a speaker for Biocodex, Danone, Sofar, Malesci, Metagenics, and Tillotts Pharma and for acting as consultant/advisor for Ferring Therapeutics, Giuliani, Metagenics, and Tillotts Pharma., (Copyright © 2023 Elsevier Inc. All rights reserved.)