Background Symbiotic relationships between animals and bacteria have profound impacts on the evolutionary trajectories of each partner. Animals and gut bacteria engage in a variety of relationships, occasionally persisting over evolutionary timescales. Ants are a diverse group of animals that engage in many types of associations with taxonomically distinct groups of bacterial associates. Here, we bring into culture and characterize two closely-related strains of gut associated Acetobacteraceae (AAB) of the red carpenter ant, Camponotus chromaiodes . Results Genome sequencing, assembly, and annotation of both strains delineate stark patterns of genomic erosion and sequence divergence in gut associated AAB. We found widespread horizontal gene transfer (HGT) in these bacterial associates and report elevated gene acquisition associated with energy production and conversion, amino acid and coenzyme transport and metabolism, defense mechanisms, and lysine export. Both strains have acquired the complete NADH-quinone oxidoreductase complex, plausibly from an Enterobacteriaceae origin, likely facilitating energy production under diverse conditions. Conservation of several lysine biosynthetic and salvage pathways and accumulation of lysine export genes via HGT implicate L-lysine supplementation by both strains as a potential functional benefit for the host. These trends are contrasted by genome-wide erosion of several amino acid biosynthetic pathways and pathways in central metabolism. We perform phylogenomic analyses on both strains as well as several free living and host associated AAB. Based on their monophyly and deep divergence from other AAB, these C. chromaiodes gut associates may represent a novel genus. Together, our results demonstrate how extensive horizontal transfer between gut associates along with genome-wide deletions leads to mosaic metabolic pathways . More broadly, these patterns demonstrate that HGT and genomic erosion shape metabolic capabilities of persistent gut associates and influence their genomic evolution. Conclusions Using comparative genomics, our study reveals substantial changes in genomic content in persistent associates of the insect gastrointestinal tract and provides evidence for the evolutionary pressures inherent to this environment. We describe patterns of genomic erosion and horizontal acquisition that result in mosaic metabolic pathways. Accordingly, the phylogenetic position of both strains of these associates form a divergent, monophyletic clade sister to gut associates of honey bees and more distantly to Gluconobacter. Electronic supplementary material The online version of this article (10.1186/s12864-019-5844-5) contains supplementary material, which is available to authorized users.

Although exclusive breastfeeding has been linked to lower rates of postnatal HIV transmission compared to nonexclusive breastfeeding, mechanisms underlying this are unclear. Across a longitudinally sampled cohort of South African infants, we showed that exclusively breastfed (EBF) infants had altered gut bacterial communities when compared to nonexclusively breastfed (NEBF) infants, as well as reduced peripheral CD4 + T cell activation and lowered chemokine and chemokine receptor expression in the oral mucosa. We further demonstrated that the relative abundance of key taxa was correlated with peripheral CD4 + T cell activation. Here, we supplement those findings by using compositional data analyses to identify shifts in the abundance of several Bifidobacteria strains relative to select strains of Escherichia, Bacteroides, and others that are associated with the transition to NEBF. We illustrate that the abundance ratio of these taxa is tightly correlated with feeding modality and is a strong predictor of peripheral T cell activation. More broadly, we discuss our study in the context of novel developments and explore future directions for the field.

word count: 241 24 Main text word count: 4,667 25 26 Abstract 29crAssphages are a class of bacteriophages that are highly abundant in the human 30 gastrointestinal tract. Accordingly, crAssphage genomes have been identified in most 31human fecal viral metagenome studies. However, we currently have an incomplete 32 understanding of factors impacting the transmission frequencies of these phages 33 between mothers and infants, and the evolutionary pressures associated with such 34 transmissions. Here, we use metagenome sequencing of stool-associated virus-like 35 particles to identify the prevalence of crAssphage across ten South African mother-36 infant dyads that are discordant for HIV infection. We report the identification of a 37 complete 97kb crAssphage genome, parts of which are detected at variable levels 38 across each mother-infant dyad. We observed average nucleotide sequence identities 39 of >99% for crAssphages from related mother-infant pairs but ~97% identities between 40 crAssphages from unrelated mothers and infants: a finding strongly suggestive of 41 vertical mother to infant transmission. We further analyzed patterns of nucleotide 42 diversity across the crAssphage sequences described here, identifying particularly 43 elevated positive selection in RNA polymerase and phage tail protein encoding genes, 44 which we validated against a crAssphage genome from previous studies. Using 16S 45 rRNA gene sequencing, we found that the relative abundances of Bacteroides 46 thetaiotaomicron and Parabacteroides merdae (Order: Bacteroidales) were differentially 47 Importance 53 crAssphages are an ubiquitous member of the human gut microbiome and modulate 54 interactions with key bacterial associates within the order Bacteroidales. However, the 55 role of this interaction in the genomic evolution of crAssphage remains unclear. Across 56 a longitudinally sampled cohort of ten South African mother-infant dyads, we use 57 metagenome sequencing of the fecal virome and 16S rRNA gene sequencing of the 58 fecal bacterial microbiota to elucidate the ecological and evolutionary dynamics of these 59interactions. Here, we demonstrate elevated levels of crAssphage average nucleotide 60 identity between related mother-infant dyads as compared to unrelated individuals, 61suggesting vertical transmission. We report strong positive selection in crAssphage 62 RNA polymerase and phage tail protein genes. Finally, we demonstrate that 63 crAssphage abundance is linearly correlated (P < 0.014) with the abundance of two 64 bacterial taxa, Bacteroides thetaiotaomicron and Parabacteroides merdae. These 65 results suggest that phage-bacterial interactions may help shape ecological and 66 evolutionary dynamics in the gut. 67 68

Effective contraceptives are a global health imperative for reproductive-aged women. However, there remains a lack of rigorous data regarding the effects of contraceptive options on vaginal bacteria and inflammation. Among 218 women enrolled into a substudy of the ECHO Trial (NCT02550067), we evaluate the effect of injectable intramuscular depot medroxyprogesterone acetate (DMPA-IM), levonorgestrel implant (LNG), and a copper intrauterine device (Cu-IUD) on the vaginal environment after one and six consecutive months of use, using 16S rRNA gene sequencing and multiplex cytokine assays. Primary endpoints include incident BV occurrence, bacterial diversity, and bacterial and cytokine concentrations. Secondary endpoints are bacterial and cytokine concentrations associated with later HIV seroconversion. Participants randomized to Cu-IUD exhibit elevated bacterial diversity, increased cytokine concentrations, and decreased relative abundance of lactobacilli after one and six months of use, relative to enrollment and other contraceptive options. Total bacterial loads of women using Cu-IUD increase 5.5 fold after six months, predominantly driven by increases in the concentrations of several inflammatory anaerobes. Furthermore, growth of L. crispatus (MV-1A-US) is inhibited by Cu2+ ions below biologically relevant concentrations, in vitro. Our work illustrates deleterious effects on the vaginal environment induced by Cu-IUD initiation, which may adversely impact sexual and reproductive health.