Happel, A.-U. | bioRxiv Science

bioRxiv2026

Relatedness of Gardnerella prophages and their endolysins

The Gardnerella genus includes a complex sub-taxonomy of bacterial species and subgroups which have been implicated in bacterial vaginosis. We analyzed G. leopoldii, G. swidsinski, G. piotii, and G. vaginalis genomes available in public databases and predicted proviral sequences using Cenote-Taker3. We clustered 266 prophage sequences into 140 viral genera level groupings that encode four distinct gene clusters and 19 different lysin proteins. Analysis of the bacterial and prophage sequence phylogenies reveals that while there were no specific prophage sequence lineages that infected each bacterial host, there is clustering of the prophage sequences by bacterial species within the Gardnerella genus.

microbiology↗

bioRxiv2026

Benchmarking virus identification tools on vaginal metagenomes

The vaginal microbiome is associated with reproductive and sexual health, yet its viral component remains understudied. A recent vaginal genome catalogue reported that 85.8% of its species-level viral groups were absent from all five viral databases examined. Viral identification tools depend on reference sequences, either directly or through their training data. Previous benchmarks used simulated or non-vaginal datasets. How well these tools generalise to vaginal metagenomes therefore remains unclear. We benchmarked 14 tools spanning five methodological approaches. Evaluations used controlled genome fragments, viral spike-in co-assemblies and virus-like particle (VLP)-enriched co-assemblies. A multi-evidence benchmark assessed 13 vaginal shotgun assemblies (primary cohort). An independent 30-sample cohort provided external validation. geNomad ranked first or second by Matthews correlation coefficient (MCC) in every ranked evaluation. VIBRANT achieved similar MCC to geNomad on the primary assemblies. It made eight false-positive calls among 11,577 negatives but recovered only 22% of viral contigs. VIBRANT ranked first in the independent cohort. Tool rankings agreed closely between cohorts (Spearman rho = 0.952; 95% CI 0.921 - 0.960). Detection of sequences lacking reference homologues differed substantially between tools. Two phage genomes without detectable reference homologues provided a controlled novelty test. Each evaluated composition-based tool recovered at least 74% of their 1,500-bp fragments. Marker- or reference-dependent tools recovered at most 31%. A separate analysis examined 48 unconfirmed candidate viral contigs lacking detectable nucleotide or protein homologues. Jaeger flagged 41, compared with four for VIBRANT and one for geNomad. On short fragments, attention-based tools achieved 4.0-5.5 times the mean area under the precision-recall curve of feature-based tools. ViraLM accounted for most of this difference. ViraLM also had the highest recall (sensitivity) of eukaryote-infecting viruses in the evaluated panel. VirSorter2 achieved the highest MCC on VLP-enriched contigs. These results support geNomad when prioritising overall classification performance and VIBRANT when minimising false-positive phage calls is the priority. ViraLM supports short-contig and eukaryote-infecting-virus detection. VirSorter2 supports identification in VLP-enriched assemblies, and Jaeger supports screening for candidate novel phages. These findings guide tool selection for studies investigating the vaginal virome in reproductive and sexual health.

microbiology↗

bioRxiv2021

Factors influencing maternal microchimerism throughout infancy and its impact on infant T cell immunity

Determinants of the acquisition and maintenance of maternal microchimerism (MMc) during infancy and the impact of MMc on infant immune responses are unknown. We examined factors which influence MMc detection and level across infancy and the effect of MMc on T cell responses to BCG vaccination in a cohort of HIV exposed, uninfected and HIV unexposed infants in South Africa. MMc was measured in whole blood from 58 infants using a panel of quantitative PCR assays at day one and 7, 15, and 36 weeks of life. Infants received BCG at birth, and selected whole blood samples from infancy were stimulated in vitro with BCG and assessed for polyfunctional CD4+ T cell responses. MMc was present in most infants across infancy with levels ranging from 0-1,193/100,000 genomic equivalents and was positively impacted by absence of maternal HIV, maternal-infant HLA compatibility, infant female sex, and exclusive breastfeeding. Initiation of maternal antiretroviral therapy prior to pregnancy partially restored MMc level in HIV exposed, uninfected infants. Birth MMc was associated with an improved polyfunctional CD4+ T cell response to BCG. These data emphasize that both maternal and infant factors influence the level of MMc, which may subsequently impact infant T cell responses. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

immunology↗