Time-Dependent Displacement of Commensal Skin Microbes by Pathogens at the Site of Colorectal Surgery

Abstract Background Although the healthy human skin microbiome has been the subject of recent studies, it is not known whether alterations among commensal microbes contribute to surgical site infections (SSIs). Our objective in this study was to characterize temporal and spatial variation in the skin microbiota of patients undergoing colorectal surgery and determine if dysbiosis contributes to SSIs. Methods Sixty one adults scheduled to undergo elective colon or rectal resection were identified by convenience sampling. By analyzing bacterial 16S rRNA gene sequences isolated from clinical samples, we used a culture-independent strategy to monitor perioperative changes in microbial diversity of fecal samples and the skin. Results A total of 990 samples from 61 patients were analyzed. Alpha diversity on the skin decreased after surgery but later recovered at the postoperative clinic visit. In most patients, we observed a transient postoperative loss of skin commensals (Corynebacterium and Propionibacterium) at the surgical site, which were replaced by potential pathogens and intestinal anaerobes (eg, Enterobacteriaceae). These changes were not observed on skin that was uninvolved in the surgical incision (chest wall). One patient developed a wound infection. Incisional skin swabs from this patient demonstrated a sharp postoperative increase in the abundance of Enterococcus, which was also cultured from wound drainage. Conclusions We observed reproducible perioperative changes in the skin microbiome following surgery. The low incidence of SSIs in this cohort precluded analysis of associations between dysbiosis and infection. We postulate that real-time monitoring of the skin microbiome could provide actionable findings about the pathogenesis of SSIs.

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Time-dependent displacement of commensal skin microbes by pathogens at the site of colorectal surgery

10.21203/rs.3.rs-34436/v1 ◽

2020 ◽

Author(s):

Jennifer Holder-Murray ◽

Andrew Yeh ◽

Matthew Rogers ◽

Brian Firek ◽

Brandon Mahler ◽

...

Keyword(s):

Colorectal Surgery ◽

Subcutaneous Fat ◽

Gastrointestinal Surgery ◽

Alpha Diversity ◽

Surgical Site Infections ◽

Perioperative Period ◽

Early Postoperative Period ◽

Rrna Gene ◽

Skin Microbiome ◽

Elective Colorectal Surgery

Abstract Objective: To characterize perioperative changes of the skin microbiome in patients undergoing elective colorectal surgery and to determine this relationship with surgical site infections (SSIs).Summary of Background Data: Despite the prevalence and significance of SSIs, their pathogenesis remains poorly understood. Although the complexity of the human skin microbiome has been the subject of recent studies, it is not known whether alterations among commensal microbes contribute to the incidence of SSIs. Methods: Skin swabs of the abdominal wall and chest wall from 60 study subjects were collected before and after colorectal surgery, in addition to intraoperative samples including subcutaneous fat and colonic contents. Bacterial 16S rRNA gene sequences were sequenced and analyzed. Results: Alpha diversity on the skin decreased in the perioperative period but later recovered at the postoperative clinic visit. Alpha diversity of the subcutaneous fat increased significantly between the beginning and end of these operations, with an increase in abundance of gut microbes also seen within luminal contents after colon resection. In the early postoperative period, the abundance of Enterobacteriaceae increased at the site of surgical incision, with a concomitant decrease in commensals including Corynebacterium and Propionibacterium. Only one patient developed a wound infection. Incisional skin swabs from this patient demonstrated a sharp postoperative increase in the abundance of Enterococcus, which was later cultured from wound drainage at the time of SSI diagnosis. Conclusions: In most patients, we observed a transient postoperative loss of skin commensals at the surgical site, which were replaced by potential pathogens and anaerobes from the gut. We postulate that real time monitoring of the skin microbiome, in parallel with improved knowledge with the gut microbiome and gastrointestinal surgery, could provide actionable findings about the pathogenesis of SSIs.

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Rhodomyrtus tomentosa Fruit Extract and Skin Microbiota: A Focus on C. acnes Phylotypes in Acne Subjects

Cosmetics ◽

10.3390/cosmetics7030053 ◽

2020 ◽

Vol 7 (3) ◽

pp. 53 ◽

Cited By ~ 1

Author(s):

Sandie Gervason ◽

Isabelle Metton ◽

Elodie Gemrot ◽

Edwige Ranouille ◽

Gilbert Skorski ◽

...

Keyword(s):

Active Ingredient ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Skin Microbiome ◽

Skin Microbiota ◽

Cutibacterium Acnes ◽

Culture Independent ◽

Rrna Gene Sequencing ◽

Abundant Genus ◽

Rhodomyrtus Tomentosa

Knowing that Rhodomyrtus tomentosa is known to have antibacterial effects, this study investigated the skin microbiota with a focus on Cutibacterium acnes (C. acnes) phylotypes in subjects with acne, and determined microbiota changes after 28 days of treatment with berries Rhodomyrtus tomentosa as an active ingredient (RT). Skin swabs from seventeen acne subjects were collected and the skin microbiome was analyzed using 16S rRNA gene sequencing. A culture-independent next-generation sequencing (NGS)-based SLST (single-locus sequence typing) approach was aimed at evaluating RT extract effects on C. acnes phylotype repartition. Clinical evaluations (lesion counts) were performed at baseline (D0) and after 28 days (D28) of twice-daily application of the RT active ingredient. We determined: (1) the skin microbiota at D0 was dominated by Actinobacteria followed by Firmicutes and Proteobacteria; (2) at the genus level, Cutibacterium was the most abundant genus followed by Staphylococcus and Corynebacterium; (3) C. acnes was the major species in terms of mean abundance, followed by Staphylococcus epidermidis (S. epidermidis) and Staphylococcus hominis (S. hominis); and (4) phylotype IA1 was most represented, with a predominance of SLST type A1, followed by phylotypes II, IB, IA2, IC, and III. After 28 days of RT extract treatment, phylotype repartition were modified with a decrease in abundance (approximately 4%) of phylotype IA1 and an increase in phylotype II and III. Cutibacterium granulosum (C. granulosum) abundance also decreased. Reduction of retentional and inflammatory lesions was also noted only after RT treatment; thus, RT extract acts as a microbiota-regulating agent.

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A contribution to the larval amphibian microbiome: characterization of bacterial microbiome of Ichthyophis bannanicus (Order: Gymnophiona) and comparison with the other two amphibian orders

10.1101/2021.09.20.461075 ◽

2021 ◽

Author(s):

Amrapali Rajput ◽

Shipeng Zhou ◽

Madhava Meegaskumbura

Keyword(s):

Gut Microbiome ◽

Alpha Diversity ◽

The Other ◽

Rrna Gene ◽

Scaling Analysis ◽

Skin Microbiome ◽

Sequencing Platform ◽

Bacterial Phyla ◽

Faecal Samples ◽

Skin Samples

It is known that animal-associated microbiomes form indispensable relationships with hosts and are responsible for many functions important for host-survival. Next-gen driven approaches documenting the remarkable diversity of microbiomes have burgeoned, with amphibians too, benefiting from such treatments. The microbiome of Gymnophiona (caecilians), one of the three amphibian orders, constituting of 3% of amphibians, however, remains almost unknown. The present study aims to address this knowledge gap through analysis of the microbiome of Ichthyophis bannanicus. As these caecilian larvae are aquatic and hence exposed to a greater propensity for bacterial microbiomic interchange, we hypothesize that bacterial phyla would overlap between gut and skin. Further, from the host-specificity patterns observed in other vertebrate taxa, we hypothesize that Gymnophiona have different dominant gut bacterial microbiomes at a higher taxonomic level when compared to the larvae of the other two amphibian orders (Anura and Caudata). We used 16S rRNA gene amplicon sequencing based on Illumina Nova sequencing platform to characterize and compare the gut (represented by faecal samples) and skin microbiome of I. bannanicus larvae (N = 13), a species distributed across South-East-Asia and the only caecilian species occurring in China. We compared our gut microbiome results with published anuran and caudate larval microbiomes. For I. bannanicus, a total of 4,053 operational taxonomic units (OTU) across 13 samples were detected. Alpha-diversity indices were significant between gut and skin samples. Non-metric multidimensional scaling analysis suggest that gut and skin samples each contained a distinct microbiome at OTU level. We record significant differences between the bacterial phyla of gut and skin samples in larvae of I. bannanicus. The study provides an overview of gut and skin bacterial microbiomes of a caecilian, while highlighting the major differences between larval microbiomes of the three amphibian orders. We find a partial overlap of gut bacterial microbiomes at phylum level for the three orders; however, the relative abundance of the dominant phyla is distinct. The skin and gut microbiomes are distinct with little overlap of species, highlighting that gut-skin axis is weak. This in turn suggests that many of the microbial species on skin and gut are functionally specialized to those locations. We also show that the skin microbiome is more diverse than the gut microbiome at species level; however, a reason for this could be a portion of the gut microbiome not being represented in faecal samples. These first microbiome information from a caecilian lay the foundation for comparative studies of the three amphibian orders.

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Surveying the sweetpotato rhizosphere, endophyte, and surrounding soil microbiomes at two North Carolina farms reveals underpinnings of sweetpotato microbiome community assembly

10.1101/758359 ◽

2019 ◽

Author(s):

C Pepe-Ranney ◽

C Keyser ◽

J Trimble ◽

B Bissinger

Keyword(s):

North Carolina ◽

Community Assembly ◽

Alpha Diversity ◽

Rrna Gene ◽

Sequence Variant ◽

Skin Microbiome ◽

Microbiome Composition ◽

Pests And Diseases ◽

Sub Saharan ◽

Surrounding Soil

AbstractFarmers grow sweetpotatoes worldwide and some sub-Saharan African and Asian diets include sweetpotato as a staple, yet the sweetpotato microbiome is conspicuously less studied relative to crops such as maize, soybean, and wheat. Studying sweetpotato microbiome ecology may reveal paths to engineer the microbiome to improve sweetpotato yield, and/or combat sweetpotato pests and diseases. We sampled sweetpotatoes and surrounding soil from two North Carolina farms. We took samples from sweetpotato fields under two different land management regimes, conventional and organic, and collected two sweetpotato cultivars, ‘Beauregard’ and ‘Covington’. By comparing SSU rRNA gene amplicon sequence profiles from sweetpotato storage root skin, rhizosphere, and surrounding soil we found the skin microbiome possessed the least composition heterogeneity among samples and lowest alpha-diversity and was significantly nested by the rhizosphere in amplicon sequence variant (ASV) membership. Many ASVs were specific to a single field and/or only found in either the skin, rhizosphere, or surrounding soil. Notably, sweetpotato skin enriched for Planctomycetaceae in relative abundance at both farms. This study elucidates underpinnings of sweetpotato microbiome community assembly, quantifies microbiome composition variance within a single farm, and reveals microorganisms associated with sweetpotato skin that belong to common but uncultured soil phylotypes.

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Effects of sampling strategy and DNA extraction on human skin microbiome investigations

Scientific Reports ◽

10.1038/s41598-019-53599-z ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 8

Author(s):

Rie Dybboe Bjerre ◽

Luisa Warchavchik Hugerth ◽

Fredrik Boulund ◽

Maike Seifert ◽

Jeanne Duus Johansen ◽

...

Keyword(s):

16S Rrna ◽

Dna Extraction ◽

Human Skin ◽

Alpha Diversity ◽

Sampling Strategy ◽

Sampling Technique ◽

Rrna Gene ◽

Skin Microbiome ◽

Library Preparation ◽

Reliable Technique

AbstractThe human skin is colonized by a wide array of microorganisms playing a role in skin disorders. Studying the skin microbiome provides unique obstacles such as low microbial biomass. The objective of this study was to establish methodology for skin microbiome analyses, focusing on sampling technique and DNA extraction. Skin swabs and scrapes were collected from 9 healthy adult subjects, and DNA extracted using 12 commercial kits. All 165 samples were sequenced using the 16S rRNA gene. Comparing the populations captured by eSwabs and scrapes, 99.3% of sequences overlapped. Using eSwabs yielded higher consistency. The success rate of library preparation applying different DNA extraction kits ranged from 39% to 100%. Some kits had higher Shannon alpha-diversity. Metagenomic shotgun analyses were performed on a subset of samples (N = 12). These data indicate that a reduction of human DNA from 90% to 57% is feasible without lowering the success of 16S rRNA library preparation and without introducing taxonomic bias. Using swabs is a reliable technique to investigate the skin microbiome. DNA extraction methodology is crucial for success of sequencing and adds a substantial amount of variation in microbiome analyses. Reduction of host DNA is recommended for interventional studies applying metagenomics.

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Microbial community compositions in breast implant biofilms associated with contracted capsules

PLoS ONE ◽

10.1371/journal.pone.0249261 ◽

2021 ◽

Vol 16 (4) ◽

pp. e0249261

Author(s):

Sean A. Crowe ◽

Rachel L. Simister ◽

Jenifer S. Spence ◽

Paul A. Kenward ◽

Aaron C. Van Slyke ◽

...

Keyword(s):

Microbial Community ◽

Bacterial Infections ◽

Breast Implant ◽

Capsular Contracture ◽

Single Species ◽

Amplicon Sequencing ◽

Complex Nature ◽

Rrna Gene ◽

Culture Independent ◽

Skin Commensals

Subclinical bacterial infections (biofilms) are strongly implicated in breast augmentation failure due to capsular contracture, and while these infections are generally ascribed to common skin commensals, this remains largely unsubstantiated through robust cultivation independent analyses. To determine capsule biofilm microbial community compositions, we employed amplicon sequencing of the 16S rRNA gene using DNA extracted from breast implant capsule samples. These cultivation independent analyses revealed that capsule associated biofilms are more diverse than canonical single-species infections, but have relatively low diversity (~ <100 species) compared to many host-associated microbial communities. In addition to taxa commonly associated with capsular contracture, the biofilms analyzed comprised a number of taxa that escaped detection in cultivation-dependent work. We have also isolated several key taxa identified through the culture-independent analyses. Together our analyses reveal that capsule biofilms are more diverse than cultivation studies suggest and can be heterogeneous within an individual capsule, between breasts of the same patient, across similar implant types, and over a range in severity of contracture. The complex nature of these communities requires further study across a broader suite of patients in addition to higher resolution analyses including metagenomics to better assess the fundamental role of microorganisms in capsular contracture.

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A Longitudinal Study of the Human Oropharynx Microbiota Over Time Reveals a Common Core and Significant Variations With Self-Reported Disease

Frontiers in Microbiology ◽

10.3389/fmicb.2020.573969 ◽

2021 ◽

Vol 11 ◽

Author(s):

Lydia Luise Bach ◽

Asha Ram ◽

Umer Z. Ijaz ◽

Thomas J. Evans ◽

Jan Lindström

Keyword(s):

Microbial Communities ◽

Community Composition ◽

Common Core ◽

Temporal Stability ◽

Alpha Diversity ◽

Molecular Techniques ◽

Human Pathogens ◽

Healthy Human ◽

Culture Independent ◽

Over Time

Our understanding of human microbial communities, in particular in regard to diseases is advancing, yet the basic understanding of the microbiome in healthy subjects over time remains limited. The oropharynx is a key target for colonization by several important human pathogens. To understand how the oropharyngeal microbiome might limit infections, and how intercurrent infections might be associated with its composition, we characterized the oropharyngeal microbiome of 18 healthy adults, sampled weekly over a 40-weeks using culture-independent molecular techniques. We detected nine phyla, 202 genera and 1438 assignments on OTU level, dominated by Firmicutes, Bacteroidetes, and Proteobacteria on phylum level. Individual microbiomes of participants were characterized by levels of high alpha diversity (mean = 204.55 OTUs, sd = 35.64), evenness (19.83, sd = 9.74) and high temporal stability (mean Pearson’s correlation between samples of 0.52, sd = 0.060), with greater differences in microbiome community composition between than within individuals. Significant changes in community composition were associated with disease states, suggesting that it is possible to detect specific changes in OTU abundance and community composition during illness. We defined the common core microbiota by varying occurrence and abundance thresholds showing that individual core microbiomes share a substantial number of OTUs across participants, chiefly Streptococci and Veillonella. Our results provide insights into the microbial communities that characterize the healthy human oropharynx, community structure and variability, and provide new approaches to define individual and shared cores. The wider implications of this result include the potential for modeling the general dynamics of oropharynx microbiota both in health and in response to antimicrobial treatments or probiotics.

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The Cutaneous Microbiome and Wounds: New Molecular Targets to Promote Wound Healing

International Journal of Molecular Sciences ◽

10.3390/ijms19092699 ◽

2018 ◽

Vol 19 (9) ◽

pp. 2699 ◽

Cited By ~ 42

Author(s):

Taylor Johnson ◽

Belinda Gómez ◽

Matthew McIntyre ◽

Michael Dubick ◽

Robert Christy ◽

...

Keyword(s):

Wound Healing ◽

Human Skin ◽

Host Immune System ◽

Skin Microbiome ◽

Epithelial Barrier Function ◽

Healing Tissue ◽

Culture Independent ◽

Skin Commensals ◽

Chronic Skin

The ecological community of microorganisms in/on humans, termed the microbiome, is vital for sustaining homeostasis. While culture-independent techniques have revealed the role of the gut microbiome in human health and disease, the role of the cutaneous microbiome in wound healing is less defined. Skin commensals are essential in the maintenance of the epithelial barrier function, regulation of the host immune system, and protection from invading pathogenic microorganisms. In this review, we summarize the literature derived from pre-clinical and clinical studies on how changes in the microbiome of various acute and chronic skin wounds impact wound healing tissue regeneration. Furthermore, we review the mechanistic insights garnered from model wound healing systems. Finally, in the face of growing concern about antibiotic-resistance, we will discuss alternative strategies for the treatment of infected wounds to improve wound healing and outcomes. Taken together, it has become apparent that commensals, symbionts, and pathogens on human skin have an intimate role in the inflammatory response that highlights several potential strategies to treat infected, non-healing wounds. Despite these promising results, there are some contradictory and controversial findings from existing studies and more research is needed to define the role of the human skin microbiome in acute and chronic wound healing.

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Nasal microbiota exhibit neither reproducible nor orderly dynamics following rhinoviral infection

10.1101/2020.04.11.20061911 ◽

2020 ◽

Author(s):

Sai N. Nimmagadda ◽

Firas S. Midani ◽

Heather Durand ◽

Aspen T. Reese ◽

Caitlin C. Murdoch ◽

...

Keyword(s):

Hypervariable Region ◽

Alpha Diversity ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Upper Respiratory Tract ◽

Healthy Human ◽

Human Volunteers ◽

Before And After ◽

Rrna Gene Sequencing ◽

Nasal Microbiota

ABSTRACTBackgroundHow human-associated microbial communities resist and respond to perturbations remains incompletely understood. Viral challenge provides one opportunity to test how human microbiota respond to disturbance.MethodsUsing an experimental human rhinovirus infection challenge model, we explored how viral infection may alter microbiota of the upper respiratory tract (URT). Healthy human volunteers were inoculated with HRV serotype 39. Samples were collected by lavage before and after inoculation from healthy (sham inoculated, n=7) and infected (n=15) individuals and subjected to 16S rRNA gene sequencing through amplification of the V4 hypervariable region.ResultsNo evidence for differences in community alpha-diversity between cohorts was observed. The composition of microbiota of sham-treated and infected subjects did not appear distinguishable and no taxa were significantly associated with infection status. We did not observe support for a correlation between microbial dynamics and counts of specific monocytes. Subject identity was found to be the strongest determinant of community structure in our dataset.ConclusionsOverall, our findings do not suggest a consistent nasopharyngeal microbiota response to rhinovirus challenge. We support the conclusion that this microbial community is individualized. Broadly, our findings contribute to our understanding of how and when immune responses to viruses affect bacterial communities in the URT.

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Surveying the Sweetpotato Rhizosphere, Endophyte, and Surrounding Soil Microbiomes at Two North Carolina Farms Reveals Underpinnings of Sweetpotato Microbiome Community Assembly

Phytobiomes Journal ◽

10.1094/pbiomes-07-19-0038-r ◽

2020 ◽

Vol 4 (1) ◽

pp. 75-89

Author(s):

C. Pepe-Ranney ◽

C. Keyser ◽

J. K. Trimble ◽

B. Bissinger

Keyword(s):

North Carolina ◽

Community Assembly ◽

Alpha Diversity ◽

Small Subunit ◽

Rrna Gene ◽

Sequence Variant ◽

Skin Microbiome ◽

Small Subunit Rrna ◽

Pests And Diseases ◽

Surrounding Soil

Farmers grow sweetpotatoes worldwide and some sub-Saharan African and Asian diets include sweetpotato as a staple, yet the sweetpotato microbiome is conspicuously less studied relative to crops such as maize, soybean, and wheat. Studying sweetpotato microbiome ecology may reveal paths to engineer the microbiome to improve sweetpotato yield, and/or combat sweetpotato pests and diseases. We sampled sweetpotatoes and surrounding soil from two North Carolina farms. We took samples from sweetpotato fields under two different land management regimes, conventional and organic, and collected two sweetpotato cultivars, ‘Beauregard’ and ‘Covington’. By comparing small subunit rRNA gene amplicon sequence profiles from sweetpotato storage root skin, rhizosphere, and surrounding soil, we found the skin microbiome possessed the least composition heterogeneity among samples, lowest alpha-diversity, and was significantly nested by the rhizosphere in amplicon sequence variant (ASV) membership. Many ASVs were specific to a single field and/or only found in either the skin, rhizosphere, or surrounding soil. Notably, sweetpotato skin enriched for Planctomycetaceae in relative abundance at both farms. This study elucidates underpinnings of sweetpotato microbiome community assembly, quantifies microbiome composition variance within a single farm, and reveals microorganisms associated with sweetpotato skin that belong to common but uncultured soil phylotypes. [Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

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