Biology subjects

Kilama, J.

Publications and source records attributed to Kilama, J..

3 recordsLinked to original sources

bioRxiv2026

Comparative Genomics of Bovine and Human Fusobacterium necrophorum Strains Reveal Subspecies- and Host-associated Differences in Virulence and Antimicrobial Resistance

Fusobacterium necrophorum (FN) is an important opportunistic pathogen implicated in necrotizing infections, including liver abscesses, calf diphtheria, metritis, and foot rot in cattle, and tonsillopharyngitis in humans. However, FN also exists as a commensal member of the bovine reproductive microbiota with potential negative, as in metritis, and even positive associations with pregnancy outcomes. The genomic features that enable FN to colonize diverse hosts and anatomical niches as either a commensal or a pathogen is poorly understood. We addressed these knowledge gaps by performing comparative genomic analysis of 137 FN strains (80 newly sequenced, 57 publicly available) from clinical and non-clinical sources across human and bovine hosts. We investigated the pangenome structure, virulence gene repertoire, antimicrobial resistance genes (ARG) prevalence, as well as host-and subspecies-associated genomic signatures of two FN subspecies: subsp. necrophorum (FNN) and subsp. funduliforme (FNF). Comparative genomics revealed an open pangenome with high accessory diversity, and phylogenetic analysis separated the strains into two distinct subspecies clades. Functional profiling revealed substantial metabolic divergence between subspecies, with FNN showing higher prevalence of carbohydrate transport systems and advanced glycation-related pathways, while FNF showed enrichment in threonate metabolism and hemolysin-related systems. Virulence gene analysis identified 84 variants across multiple functional categories with subspecies- and host-specific distributions. Antimicrobial resistance genes, primarily tetracycline resistance genes [tet(O), tet(M), tet(40)] and the macrolide resistance gene erm(B), were detected in 22.6% of strains, with higher prevalence in bovine than human strains. Overall, our results suggest that pathogenic potential of FN appears to be determined by the interplay between an open pangenome, subspecies-specific metabolic and virulence repertoires, host-associated adaptation, and niche specialization. IMPORTANCEFusobacterium necrophorum, comprising two subspecies, necrophorum (FNN) and funduliforme (FNF), is a major pathogen in cattle and humans, yet it also occurs as a commensal inhabitant in healthy cattle, particularly in the rumen, hindgut, semen, and the female reproductive tract. However, emerging evidence indicates it also occurs as a non-clinical inhabitant, particularly in the bovine reproductive tract, where it may be associated with improved pregnancy outcomes. We conducted a comparative genomic analysis of 137 F. necrophorum strains, including FNN (n = 12) and FNF (n = 125), sourced from humans (n=53) and cattle (n=84) across seven anatomical niches spanning both healthy and diseased sources. We identified subspecies- and host-specific metabolic pathways, antimicrobial resistance profiles, and distinct virulence gene distributions that underpin the ecological versatility of Fusobacterium necrophorum. Overall, these findings provide a genomic framework for understanding its host adaptation and niche specialization across bovine and human hosts.

microbiology↗

bioRxiv2026

Vaginal and uterine microbiomes in beef cattle at artificial insemination and associations with pregnancy outcomes

The female reproductive tract harbors complex microbial communities that may influence reproductive success. In previous work using 16S rRNA gene sequencing, we identified bacterial taxa in the vagina and uterus of beef cattle associated with pregnancy outcomes, but taxonomic resolution and functional inference was limited. Here we used shotgun metagenomic sequencing to characterize the taxonomic composition, functional potential, and antimicrobial resistome of vaginal and uterine microbiomes at the time of artificial insemination (AI) in cows that subsequently became pregnant or remained open. Vaginal (pregnant n = 54; open n = 7) and uterine (pregnant, n = 41; open, n = 9) samples were collected prior to AI. Microbial community structure did not differ between pregnancy outcome groups in either anatomical site (PERMANOVA; P > 0.05). However, cows that remained open showed significantly greater species-level richness and diversity in the vaginal microbiome (P < 0.05). No diversity differences were observed in the uterine microbiome. In contrast, significant differences were detected between anatomical sites, with distinct dominant taxa and functional profiles. Vaginal microbiomes were enriched in pathways related to genetic information processing, whereas uterine microbiomes exhibited greater representation of metabolic pathways. A total of 105 ARGs spanning 11 antimicrobial classes were identified, with tetracycline resistance genes [tet(Q), tet(W), and tet(M)] predominating, and blaTEM-116 more abundant in the uterine microbiome. Overall, while vaginal and uterine microbiomes were compositionally and functionally distinct, no robust pregnancy-associated taxonomic or functional signatures were detected, likely reflecting limited statistical power and challenges inherent to low-biomass metagenomic datasets. IMPORTANCEUnderstanding the role of the reproductive tract microbiome in fertility could improve reproductive efficiency in cattle. We used shotgun metagenomic sequencing to characterize the taxonomic composition, functional potential, and antimicrobial resistome of vaginal and uterine microbiomes at the time of artificial insemination in cows that subsequently became pregnant or remained open. Using paired samples from the same animals, we directly compared microbial communities between the upper and lower reproductive tract to identify shared and site-specific features. Although no distinct microbial signatures associated with pregnancy outcomes were detected, this may reflect limited statistical power and low microbial biomass inherent to these samples. Despite these challenges, our study provides high-resolution insights into the composition, functional potential, and resistome of bovine reproductive microbiomes and highlights important technical considerations for studying low-biomass microbial ecosystems.

microbiology↗

bioRxiv2024

Fusobacterium necrophorum and Fusobacterium varium are commensal members of the bovine reproductive microbiota and may colonize calf prenatally

Fusobacterium necrophorum is an important pathogen associated with several infectious diseases in cattle. However, recent sequencing-based studies have indicated that F. necrophorum is positively associated with pregnancy in beef cows and that Fusobacterium is the most abundant genus in the bull seminal microbiota, suggesting the potential role of Fusobacterium in reproductive health and fertility. Here, we performed a comprehensive screening to 1) determine whether Fusobacterium necrophorum (subspecies necrophorum [FNN] and funduliforme [FNF]), and Fusobacterium varium (FV) are part of the commensal members of the reproductive microbiota in cattle; 2) to explore whether these Fusobacterium spp. are colonized in calf prenatally. For this, we screened 11 different sample types including bovine and ram semen, bovine vaginal and uterine swabs, and bull fecal samples, as well as samples from 180- and 260-days old calf fetuses and their respective dams using both quantitative PCR (514 samples) and targeted culturing (499 samples). By qPCR, all the targeted Fusobacterium spp. were detected across all sample types, with FNF being the highly prevalent in the bull semen (66.7%) and maternal ruminal fluids (87.1%), which was confirmed by culturing. All the targeted Fusobacterium were identified in vaginal and uterine (3.1%-9.4%) as well as placental caruncles, and fetal fluids, ruminal and meconium samples (2.7% - 26.3%) by qPCR and were not isolated by culture method. Overall, our results suggest that F. necrophorum is a commensal member of healthy male reproductive microbiota, and that FNF, FNN and FV are present in bovine vagino-uterine microbiota, and calf intestine prenatally.

microbiology↗