The microbiome in wound repair and tissue fibrosis

Bacterial colonization occurs in all wounds, chronic or acute, and the break in epithelium integrity that defines a wound impairs the forces that shape and constrain the microbiome at that site. This review highlights the interactions between bacterial communities in the wound and the ultimate resolution of the wound or development of fibrotic lesions. Chronic wounds support complex microbial communities comprising a wide variety of bacterial phyla, genera, and species, including some fastidious anaerobic bacteria not identified using culture‐based methods. Thus, the complexity of bacterial communities in wounds has historically been underestimated. There are a number of intriguing possibilities to explain these results that may also provide novel insights into changes and adaptation of bacterial metabolic networks in inflamed and wounded mucosa, including the critical role of biofilm formation. It is well accepted that the heightened state of activation of host cells in a wound that is driven by the microbiota can certainly lead to detrimental effects on wound regeneration, but the microbiota of the wound may also have beneficial effects on wound healing. Studies in experimental systems have clearly demonstrated a beneficial effect for members of the gut microbiota on regulation of systemic inflammation, which could also impact wound healing at sites outside the gastrointestinal tract. The utilization of culture‐independent microbiology to characterize the microbiome of wounds and surrounding mucosa has raised many intriguing questions regarding previously held notions about the cause and effect relationships between bacterial colonization and wound repair and mechanisms involved in this symbiotic relationship.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95009/1/path4118.pd

A tale of two sites: how inflammation can reshape the microbiomes of the gut and lungs

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141495/1/jlb0943.pd

Cross-Hemisphere Study Reveals Geographically Ubiquitous, Plastic-Specific Bacteria Emerging from the Rare and Unexplored Biosphere

While it is now appreciated that the millions of tons of plastic pollution travelling through marine systems carry complex communities of microorganisms, it is still unknown to what extent these biofilm communities are specific to the plastic or selected by the surrounding ecosystem. To address this, we characterized and compared the microbial communities of microplastic particles, nonplastic (natural and wax) particles, and the surrounding waters from three marine ecosystems (the Baltic, Sargasso and Mediterranean seas) using high-throughput 16S rRNA gene sequencing. We found that biofilm communities on microplastic and nonplastic particles were highly similar to one another across this broad geographical range. The similar temperature and salinity profiles of the Sargasso and Mediterranean seas, compared to the Baltic Sea, were reflected in the biofilm communities. We identified plastic-specific operational taxonomic units (OTUs) that were not detected on nonplastic particles or in the surrounding waters. Twenty-six of the plastic-specific OTUs were geographically ubiquitous across all sampled locations. These geographically ubiquitous plastic-specific OTUs were mostly low-abundance members of their biofilm communities and often represented uncultured members of marine ecosystems. These results demonstrate the potential for plastics to be a reservoir of rare and understudied microbes, thus warranting further investigations into the dynamics and role of these microbes in marine ecosystems

Comparative genomics of Pseudomonas fluorescens subclade III strains from human lungs

Abstract Background While the taxonomy and genomics of environmental strains from the P. fluorescens species-complex has been reported, little is known about P. fluorescens strains from clinical samples. In this report, we provide the first genomic analysis of P. fluorescens strains in which human vs. environmental isolates are compared. Results Seven P. fluorescens strains were isolated from respiratory samples from cystic fibrosis (CF) patients. The clinical strains could grow at a higher temperature (>34 °C) than has been reported for environmental strains. Draft genomes were generated for all of the clinical strains, and multi-locus sequence analysis placed them within subclade III of the P. fluorescens species-complex. All strains encoded type- II, −III, −IV, and -VI secretion systems, as well as the widespread colonization island (WCI). This is the first description of a WCI in P. fluorescens strains. All strains also encoded a complete I2/PfiT locus and showed evidence of horizontal gene transfer. The clinical strains were found to differ from the environmental strains in the number of genes involved in metal resistance, which may be a possible adaptation to chronic antibiotic exposure in the CF lung. Conclusions This is the largest comparative genomics analysis of P. fluorescens subclade III strains to date and includes the first clinical isolates. At a global level, the clinical P. fluorescens subclade III strains were largely indistinguishable from environmental P. fluorescens subclade III strains, supporting the idea that identifying strains as ‘environmental’ vs ‘clinical’ is not a phenotypic trait. Rather, strains within P. fluorescens subclade III will colonize and persist in any niche that provides the requirements necessary for growth.http://deepblue.lib.umich.edu/bitstream/2027.42/116129/1/12864_2015_Article_2261.pd

Vibrio Colonization Is Highly Dynamic in Early Microplastic-Associated Biofilms as Well as on Field-Collected Microplastics

Microplastics are ubiquitous in aquatic ecosystems and provide a habitat for biofilm-forming bacteria. The genus Vibrio, which includes potential pathogens, was detected irregularly on microplastics. Since then, the potential of microplastics to enrich (and serve as a vector for) Vibrio has been widely discussed. We investigated Vibrio abundance and operational taxonomic unit (OTU) composition on polyethylene and polystyrene within the first 10 h of colonization during an in situ incubation experiment, along with those found on particles collected from the Baltic Sea. We used 16S rRNA gene amplicon sequencing and co-occurrence networks to elaborate the role of Vibrio within biofilms. Colonization of plastics with Vibrio was detectable after one hour of incubation; however, Vibrio numbers and composition were very dynamic, with a more stable population at the site with highest nutrients and lowest salinity. Likewise, Vibrio abundances on field-collected particles were variable but correlated with proximity to major cities. Vibrio was poorly connected within biofilm networks. Taken together, this indicates that Vibrio is an early colonizer of plastics, but that the process is undirected and independent of the specific surface. Still, higher nutrients could enhance a faster establishment of Vibrio populations. These parameters should be considered when planning studies investigating Vibrio on microplastics

Hunting for pigments in bacterial settlers of the Great Pacific Garbage Patch

Scales BS, Hassenrück C, Moldaenke L, et al. Hunting for pigments in bacterial settlers of the Great Pacific Garbage Patch. Environmental Microbiology. 2024;26(6).The Great Pacific Garbage Patch, a significant collection of plastic introduced by human activities, provides an ideal environment to study bacterial lifestyles on plastic substrates. We proposed that bacteria colonizing the floating plastic debris would develop strategies to deal with the ultraviolet‐exposed substrate, such as the production of antioxidant pigments. We observed a variety of pigmentation in 67 strains that were directly cultivated from plastic pieces sampled from the Garbage Patch. The genomic analysis of four representative strains, each distinct in taxonomy, revealed multiple pathways for carotenoid production. These pathways include those that produce less common carotenoids and a cluster of photosynthetic genes. This cluster appears to originate from a potentially new species of theRhodobacteraceaefamily. This represents the first report of an aerobic anoxygenic photoheterotrophic bacterium from plastic biofilms. Spectral analysis showed that the bacteria actively produce carotenoids, such as beta‐carotene and beta‐cryptoxanthin, and bacteriochlorophyll a. Furthermore, we discovered that the genetic ability to synthesize carotenoids is more common in plastic biofilms than in the surrounding water communities. Our findings suggest that plastic biofilms could be an overlooked source of bacteria‐produced carotenoids, including rare forms. It also suggests that photoreactive molecules might play a crucial role in bacterial biofilm communities in surface water

Changes in the Lung Microbiome following Lung Transplantation Include the Emergence of Two Distinct Pseudomonas Species with Distinct Clinical Associations

<div><p>Background</p><p>Multiple independent culture-based studies have identified the presence of <i>Pseudomonas aeruginosa</i> in respiratory samples as a positive risk factor for bronchiolitis obliterans syndrome (BOS). Yet, culture-independent microbiological techniques have identified a negative association between <i>Pseudomonas</i> species and BOS. Our objective was to investigate whether there may be a unifying explanation for these apparently dichotomous results.</p><p>Methods</p><p>We performed bronchoscopies with bronchoalveolar lavage (BAL) on lung transplant recipients (46 procedures in 33 patients) and 26 non-transplant control subjects. We analyzed bacterial communities in the BAL fluid using qPCR and pyrosequencing of 16S rRNA gene amplicons and compared the culture-independent data with the clinical metadata and culture results from these subjects.</p><p>Findings</p><p>Route of bronchoscopy (via nose or via mouth) was not associated with changes in BAL microbiota (p = 0.90). Among the subjects with positive <i>Pseudomonas</i> bacterial culture, <i>P. aeruginosa</i> was also identified by culture-independent methods. In contrast, a distinct <i>Pseudomonas</i> species, <i>P. fluorescens</i>, was often identified in asymptomatic transplant subjects by pyrosequencing but not detected via standard bacterial culture. The subject populations harboring these two distinct pseudomonads differed significantly with respect to associated symptoms, BAL neutrophilia, bacterial DNA burden and microbial diversity. Despite notable differences in culturability, a global database search of UM Hospital Clinical Microbiology Laboratory records indicated that <i>P. fluorescens</i> is commonly isolated from respiratory specimens.</p><p>Interpretation</p><p>We have reported for the first time that two prominent and distinct <i>Pseudomonas</i> species (<i>P. fluorescens</i> and <i>P. aeruginosa</i>) exist within the post-transplant lung microbiome, each with unique genomic and microbiologic features and widely divergent clinical associations, including presence during acute infection.</p></div

Percentage of Subjects with >10% Relative Abundance of Prominent Genera.

<p>Percentage of Subjects with >10% Relative Abundance of Prominent Genera.</p

Culture Results of Lung Transplant BAL Specimens.

<p>Culture Results of Lung Transplant BAL Specimens.</p

Abundance and Identification of Prominent Pseudomonas OTUs in Lung Transplant BALs<b>.</b>

<p>1: All BALs with OTU 1065 as the most abundant OTU grew <i>P. aeruginosa</i>. No BALs with either other OTU as the most abundant had positive cultures; 2: Of the 10 completed genomes in the database with 100% homology and 100% identity, nine were <i>P. aeruginosa</i>. 3: Of the two completed genomes in the database with 100% homology and 100% identity, one was <i>P. fluorescens</i> and one was <i>P. poae</i>, a recently described member of the <i>P. fluorescens</i> group (<a href="http://www.uniprot.org/taxonomy/200451" target="_blank">http://www.uniprot.org/taxonomy/200451</a>); 4: No BLAST matches met 100% identity and homology. The genomes with the highest identity and homology were exclusively members of the <i>P. fluorescens</i> group.</p