Biology subjects

Swaney, M. H.

Publications and source records attributed to Swaney, M. H..

4 recordsLinked to original sources

bioRxiv2022

Comparative genomic and metagenomic investigations of the Corynebacterium tuberculostearicum species complex reveals potential mechanisms underlying associations to skin health and disease

Corynebacterium are a diverse genus and dominant member of the human skin microbiome. Recently, we reported that the most prevalent Corynebacterium species found on skin - including Corynebacterium tuberculostearicum and Corynebacterium kefirresidentii - comprise a narrow species complex despite the diversity of the genus. Here, we apply high-resolution phylogenomics and comparative genomics to describe the structure of the C. tuberculostearicum species complex. We find this species complex is missing a fatty acid biosynthesis gene family which is often found in multi-copy in approximately 99% of other Corynebacterium species. Conversely, this species complex is enriched for multiple genetic traits, including a gene encoding for a collagen-like peptide. Further, through metagenomic investigations, we find that one species within the complex, C. kefirresidentii, increases in relative abundance during atopic dermatitis flares and show that most members of this species possess a colocalized set of putative virulence genes.

microbiology↗

bioRxiv2022

Sweat and sebum preferences of the human skin microbiota

The microorganisms that inhabit human skin, collectively termed the skin microbiome, must overcome numerous challenges that typically impede microbial growth, including low pH, osmotic pressure, and low nutrient availability. Yet, the skin microbiota thrive on the skin and have adapted to these stressful conditions. Limited skin nutrients are available for microbial use in this unique niche, including those from host-derived sweat, sebum, and corneocytes. Here, we have developed physiologically-relevant, skin-like growth media that is composed of compounds present in human sweat and sebum. We find that skin-associated bacterial species exhibit unique growth profiles in different concentrations of sweat and sebum. The majority of strains evaluated demonstrate a preference for high sweat concentrations, while sebum preference is highly variable, suggesting that the capacity for sebum utilization may be an important driver of skin microbial community structure. Furthermore, these findings provide experimental rationale for why different skin microenvironments harbor distinct microbiome communities. In all, our study further emphasizes the importance of studying microorganisms in an ecologically-relevant context, which is critical for our understanding of their physiology, ecology, and function on the skin.

microbiology↗

bioRxiv2022

lsaBGC provides a comprehensive framework for evolutionary analysis of biosynthetic gene clusters within focal taxa

We developed lsaBGC, a bioinformatics suite that introduces several new methods to expand on the available infrastructure for genomic and metagenomic-based comparative and evolutionary investigation of biosynthetic gene clusters (BGCs). Through application of the suite to four genera commonly found in skin microbiomes, we uncover multiple novel findings on the evolution and diversity of their BGCs. We show that the virulence associated carotenoid staphyloxanthin in Staphylococcus aureus is ubiquitous across the Staphylococcus genus but has largely been lost in the skin-commensal species Staphylococcus epidermidis. We further identify thousands of novel single nucleotide variants (SNVs) within BGCs from the Corynebacterium tuberculostearicum sp. complex, which we describe here to be a narrow, multi-species clade that features the most prevalent Corynebacterium in healthy skin microbiomes. Although novel SNVs were approximately ten times as likely to correspond to synonymous changes when located in the top five percentile of conserved sites, lsaBGC identified SNVs which defied this trend and are predicted to underlie amino acid changes within functionally key enzymatic domains. Ultimately, beyond supporting evolutionary investigations, lsaBGC provides important functionalities to aid efforts for the discovery or synthesis of natural products.

microbiology↗

bioRxiv2020

Corynebacterium Comparative Genomics Reveals a Role for Cobamide Sharing in the Skin Microbiome

The human skin microbiome is a key player in human health, with diverse functions ranging from defense against pathogens to education of the immune system. While recent studies have begun to shed light on the valuable role that skin microorganisms have in maintaining a healthy skin barrier, a detailed understanding of the complex interactions that shape healthy skin microbial communities is limited. Cobamides, the vitamin B12 class of cofactor, are essential for organisms across the tree of life. Because this vitamin is only produced by a limited fraction of prokaryotes, cobamide sharing has been shown to mediate community dynamics within microbial communities. Here, we provide the first large-scale unbiased metagenomic assessment of cobamide biosynthesis and utilization in the skin microbiome. We show that while numerous and diverse taxa across the major bacterial phyla on the skin are cobamide dependent, relatively few species encode for de novo cobamide biosynthesis. We find that cobamide sharing shapes the network structure in microbial communities across the different microenvironments of the skin and that changes in community structure and microbiome diversity are driven by the abundance of cobamide producers in the Corynebacterium genus, in both healthy and disease skin states. Lastly, we find that de novo cobamide biosynthesis is enriched only in host-associated Corynebacterium species, including those prevalent on human skin. We confirm that the cofactor is produced in excess through quantification of cobamide production by skin-associated species isolated in the laboratory. Taken together, our results support a role for cobamide sharing within skin microbial communities, which we predict stabilizes the microbiome and mediates host interactions.

microbiology↗