Differences In Microbial Composition Research Articles

Understanding the microbial biogeography of ancient human dentitions to guide study design and interpretation.

The oral cavity is a heterogeneous environment, varying in factors such as pH, oxygen levels, and salivary flow. These factors affect the microbial community composition and distribution of species in dental plaque, but it is not known how well these patterns are reflected in archaeological dental calculus. In most archaeological studies, a single sample of dental calculus is studied per individual and is assumed to represent the entire oral cavity. However, it is not known if this sampling strategy introduces biases into studies of the ancient oral microbiome. Here, we present the results of a shotgun metagenomic study of a dense sampling of dental calculus from four Chalcolithic individuals from the southeast Iberian peninsula (ca. 4500-5000 BP). Interindividual differences in microbial composition are found to be much larger than intraindividual differences, indicating that a single sample can indeed represent an individual in most cases. However, there are minor spatial patterns in species distribution within the oral cavity that should be taken into account when designing a study or interpreting results. Finally, we show that plant DNA identified in the samples is likely of postmortem origin, demonstrating the importance of including environmental controls or additional lines of biomolecular evidence in dietary interpretations.

Involvement of Abnormal Gut Microbiota Composition and Function in Doxorubicin-Induced Cardiotoxicity

ObjectivesDoxorubicin (Dox), a chemotherapeutic anthracycline agent for the treatment of a variety of malignancies, has a limitation in clinical application for dose-dependent cardiotoxicity. The purpose of this study was to explore the relationship between the composition/function of the gut microbiota and Dox-induced cardiotoxicity (DIC).MethodsC57BL/6J mice were injected intraperitoneally with 15 mg/kg of Dox, with or without antibiotics (Abs) administration. The M-mode echocardiograms were performed to assess cardiac function. The histopathological analysis was conducted by H&E staining and TUNEL kit assay. The serum levels of creatine kinase (CK), CK-MB (CK-MB), lactic dehydrogenase (LDH), and cardiac troponin T (cTnT) were analyzed by an automatic biochemical analyzer. 16S rRNA gene and metagenomic sequencing of fecal samples were used to explore the gut microbiota composition and function.Key FindingsDox caused left ventricular (LV) dilation and reduced LV contractility. The levels of cardiomyocyte apoptosis and myocardial enzymes were elevated in Dox-treated mice compared with the control (Con) group. 16S rRNA gene sequencing results revealed significant differences in microbial composition between the two groups. In the Dox group, the relative abundances of Allobaculum, Muribaculum, and Lachnoclostridium were significantly decreased, whereas Faecalibaculum, Dubosiella, and Lachnospiraceae were significantly increased compared with the Con group at the genus level. Functional enrichment with Cluster of orthologous groups of proteins (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the Dox mice displayed different clusters of cellular processes and metabolism from the Con mice. The different species and their functions between the two groups were associated with the clinical factors of cardiac enzymes. Moreover, depletion of the gut microbiota could alleviate Dox-induced myocardial injury and cardiomyocyte apoptosis.ConclusionsThe study here shows that composition imbalance and functional changes of the gut microbiota can be one of the etiological mechanisms underlying DIC. The gut microbiota may serve as new targets for the treatment of cardiotoxicity and cardiovascular diseases.

Microbiomes of Healthy and Bleached Corals During a 2016 Thermal Bleaching Event in the Andaman Sea of Thailand

As seawater temperature rises, repeated thermal bleaching events have negatively affected the reefs of the Andaman Sea for over decades. Studies on the coral-associated microbial diversity of prokaryotes and microbial eukaryotes (microbiome) in healthy and bleached corals are important to better understand the coral holobionts that involved augmented resistance to stresses, and this information remains limited in the Andaman Sea of Thailand. The present study thereby described the microbiomes of healthy (unbleached) and bleached colonies of four prevalent corals, Acropora humilis, Platygyra sp., Pocillopora damicornis, and Porites lutea, along with the surrounding seawater and sediments, that were collected during a 2016 thermal bleaching event, using 16S and 18S rRNA genes next-generation sequencing (NGS). Both prokaryotic and eukaryotic microbes showed isolated community profiles among sample types (corals, sediment, and seawater) [analysis of similarities (ANOSIM): p = 0.038 for prokaryotes, p < 0.001 for microbial eukaryotes] and among coral genera (ANOSIM: p < 0.001 for prokaryotes and microbial eukaryotes). In bleached state corals, we found differences in microbial compositions from the healthy state corals. Prevalent differences shared among bleached coral genera (shared in at least three coral genera) included a loss of reported coral-beneficial microbes, such as Pseudomonadales, Alteromonadales, and Symbiodinium; meanwhile an increase of putative coral-pathogenic Malassezia and Aspergillus. This difference could affect carbon and nitrogen availability for coral growth, reflective of a healthy or bleached state. Our findings in part supported previously microbial dysbiosis knowledge of thermal bleaching coral microbiomes around South East Asia marine geography, and together ongoing efforts are to support the understanding and management of microbial diversity to reduce the negative impacts to corals in massive thermal bleaching events.

Profiling the Bladder Microbiota in Patients With Bladder Cancer.

Evidence suggests that microbiota may contribute to the pathogenesis of several diseases, including cancer. In the case of bladder cancer, preliminary studies have found alterations in the urinary microbiota of patients with urothelial carcinoma compared with healthy individuals. Conversely, the urinary microbiota differ between men and women, and it has been hypothesized that these differences are associated with the lower incidence of bladder cancers in women. The objective of this study was to characterize the bladder microbiota in paired samples of tumor and non-tumor mucosa of patients with malignant bladder neoplasia using next-generation sequencing. In addition, we aimed to study potential differences in microbial composition in tumor samples according to clinical and pathological variables, and to determine possible microbial profiles. We found significant differences in microbial richness at the genus level, with a higher richness observed in the non-tumor compared with the tumor mucosa. It was also shown that Actinobacteria were significantly more enriched in the non-tumor compared with the tumor mucosa (P = 0.014). In the multivariate analysis, we found significant differences in microbial composition according to tumor grade (P = 0.03 and 0.04 at the phylum and genus levels, respectively). Moreover, we detected a higher microbial richness in non-tumor vs. tumor tissues which agrees with the global assumption that microbial richness is an indicator of health. The greater abundance of members of the Actinobacteria phylum in the non-neoplastic bladder mucosa samples supports the hypothesis that a higher abundance of Actinomycetes is associated with a lower rate of bladder cancer in women and suggests a protective role for these microbiota. We detected a microbial profile that was enriched for Enterococcus in low-grade tumors. Finally, we identified the presence of two clusters in the microbial composition of the tumor mucosa samples, significantly enriched for the genera Barnesiella, Parabacteroides, Prevotella, Alistipes, and Lachnospiracea_incertae_sedis (Cluster 1), or Staphylococcus (Cluster 2). Further longitudinal studies are needed to assess the role of the bladder microbiota in carcinogenesis.

Soil microbial community development across a 32-year coastal wetland restoration time series and the relative importance of environmental factors

Soil microbes play key roles in ecosystem functioning through processes such as organic matter decomposition, nutrient and carbon cycling, and regulating vegetation structure and productivity. Coastal marshes are situated at the confluence of terrestrial and marine ecosystems; thus, their soils support abundant and diverse microbiota which facilitate globally important biogeochemical processes including nutrient cycling and greenhouse gas fluxes. With coastal marsh ecosystems threatened by relative sea level rise, subsidence, and development, mitigation for the loss of marshes is becoming commonplace. Despite the widespread implementation of marsh construction projects, little is known about the development and variability of microbial communities in created marshes. For this study, we tested the hypothesis that microbial community composition differs across created marshes of different ages and between created and natural marshes. We also hypothesized that the microbial community would be correlated with soil properties including soil organic carbon and nitrogen content, which were predicted to increase with marsh age. To test these hypotheses, we determined dominant microbial groups and environmental characteristics from six constructed marshes ranging in age from 0 to 32 years old, as well as an adjacent natural marsh. Our results revealed that microbial biomass estimates increased with marsh age except for the high elevation 20-year old marsh, yet each marsh contained a distinct microbial community composition. Across marshes, microbial community composition was significantly related to soil C:N ratio with an increase in total microbial abundance and actinomycetes and GM+ bacteria with an increase in soil C to N ratio. Additionally, shifts in dominant microbial groups were associated with differences in vegetation, elevation, and marsh age. The natural marsh community grouped more closely with younger rather than older marshes suggesting age is less important than environmental conditions. This study shows that microbial communities are not homogenized across restoration sites and do not necessarily converge to be similar to natural marshes over time. Local biotic and environmental conditions were correlated with microbial compositions, yet in seemingly similar conditions, microbial groups also differed. The effect of differences in microbial compositions on ecological functions are yet to be fully understood.

INTESTINAL EPITHELIAL CELL-SPECIFIC CFTR KNOCKOUT MICE EXHIBIT FECAL MICROBIAL DYSBIOSIS

Abstract BACKGROUND Chronic intestinal inflammation is a poorly understood manifestation of Cystic Fibrosis (CF) disease. Fecal microbial dysbiosis has the potential of inducing intestinal inflammation and has been reported in people with CF as well as CF mouse models. CF mice consuming an osmotic polyethylene glycol (PEG) laxative in drinking water to prevent intestinal obstruction have low levels of intestinal inflammation and low intestinal bacterial loads. In contrast, CF mice consuming a nutritionally complete liquid diet to prevent intestinal impaction exhibit intestinal inflammation and high intestinal bacterial loads (R. C. De Lisle, et al., Am J Physiol 293, G577-G584, 2007) To investigate the development of dysbiosis in a CFTR-deficient intestine, we transitioned adult intestinal epithelial cell-specific knockout and wild-type (WT) mice from life-long consumption of PEG laxative to a nutritionally-complete liquid diet for a two week period before collection of fecal samples. METHODS Fecal samples collected from B6.Cg-Tg(Vil1-cre)-Cftrf10/f10 intestinal-specific Cftr knockout mice (iCftr KO) and their WT sex-matched littermates were DNA extracted and prepared for 16S rRNA sequencing and evaluation of the microbiome. Microbial community composition, richness and diversity indices, and relative abundance of bacterial species of interest were evaluated. RESULTS 16S rRNA sequencing and metagenomic analysis revealed significant differences in microbial composition with intestinal-specific loss of CFTR as compared to WT, as well as a significant decrease in Shannon diversity and Chao-1 richness indices. A significant deficit of taxa was seen in the intestinal-specific CF mice, as compared to WT, which corresponded with a significant increase in bacterial species that potentially serve as provocateurs of intestinal inflammation including Helicobacter typhlonius, Clostridium perfringens, Ruminococcus gnavus, and Tyzerella spp. CONCLUSIONS As compared to WT, the transition from PEG laxative to a nutritionally-complete liquid diet resulted in overt differences in the fecal microbiota composition in iCftr KO mice which included enrichment of potential bacterial pathobionts capable of stimulating intestinal inflammation. These studies suggest that the CFTR-deficient intestinal epithelium provides an environment selective for potential bacterial pathobionts. The paradigm of the study may prove useful for investigating the development of dysbiosis and corresponding changes in intestinal mucosal immunity.

Microbiome changes in the gastric mucosa and gastric juice in different histological stages of Helicobacter pylori-negative gastric cancers.

BACKGROUNDThe gastric microbiota in patients with gastric cancer (GC) has received increasing attention, but the profiling of the gastric microbiome through the histological stages of gastric tumorigenesis remains poorly understood, especially for patients with Helicobacter pylori-negative GC (HPNGC).AIMTo characterize microbial profiles of gastric mucosa and juice for HPNGC carcinogenesis and identify distinct taxa in precancerous lesions.METHODSThe 16S rRNA gene analysis was performed on gastric mucosa from 134 Helicobacter pylori-negative cases, including 56 superficial gastritis (SG), 9 atrophic gastritis (AG), 27 intestinal metaplasia (IM), 29 dysplasia (Dys), and 13 GC cases, to investigate differences in gastric microbial diversity and composition across the disease stages. In addition, paired gastric mucosa and juice samples from 18 SG, 18 IM, and 18 Dys samples were analyzed. α-Diversity was measured by Shannon and Chao1 indexes, and β-diversity was calculated using partial least squares discrimination analysis (PLS-DA). Differences in the microbial composition across disease stages in different sample types were assessed using the linear discriminant analysis effect size.RESULTSThe diversity and composition of the bacterial microbiota in the gastric mucosa changed progressively across stages of gastric carcinogenesis. The diversity of the gastric mucosa microbiota was found to be significantly lower in the IM and Dys groups than in the SG group, and the patients with GC had the lowest bacterial community richness (P < 0.05). Patients with IM and those with Dys had similar gastric mucosa microbiota profiles with Ralstonia and Rhodococcus as the predominant genera. Microbial network analysis showed that there was increasing correlation strength between IM and Dys (|correlation threshold|≥ 0.5, P < 0.05). GC and its precancerous lesions have distinguishable bacterial taxa; our results identified HPNGC-associated bacteria Streptococcaceae and Lactobacillaceae (P < 0.05). Additionally, across precancerous lesion stages from AG to Dys in Helicobacter pylori-negative patients, Burkholderiaceae abundance continuously increased, while Streptococcaceae and Prevotellaceae abundance presented a continuous downward trend. Furthermore, the microbial diversity was higher in gastric juice (P < 0.001) than in the mucosa, while PLS-DA revealed a statistically significant difference between the two groups (ANOSIM, P = 0.001). A significant difference in the microbial structure was identified, with Proteobacteria being more prevalent in the gastric mucosa and Firmicutes being more abundant in gastric juice.CONCLUSIONOur results provide insights into potential taxonomic biomarkers for HPNGC and its precancerous stages and assist in predicting the prognosis of IM and Dys based on the mucosal microbiota profile.

Anemochore Seeds Harbor Distinct Fungal and Bacterial Abundance, Composition, and Functional Profiles.

Many plants adapted to harsh environments have evolved low seed mass (‘light seeds’) with specific dispersal strategies, primarily either by wind (anemochory) or water (hydrochory). However, the role of their seed microbiota in their survival, and their seed microbial abundance and structure, remain insufficiently studied. Herein, we studied the light seed microbiome of eight anemochores and two hydrochores (as controls) collected from four provinces in China, using qPCR and metagenomic sequencing targeting both bacteria and fungi. Substantial variations were found for seed endophytic fungi (9.9 × 1010~7.3 × 102 gene copy numbers per seed) and bacteria (1.7 × 1010~8.0 × 106). Seed microbial diversity and structure were mainly driven by the plant genotype (species), with weak influences from their host plant classification level or dispersal mode. Seed microbial composition differences were clear at the microbial phylum level, with dominant proportions (~75%) for Proteobacteria and Ascomycota. The light seeds studied harbored unique microbial signatures, sharing only two Halomonas amplicon sequence variants (ASVs) and two fungal ASVs affiliated to Alternaria and Cladosporium. A genome-level functional profile analysis revealed that seed bacterial microbiota were enriched in amino acid, nucleoside, and nucleotide biosynthesis, while in fungal communities the generation of precursor metabolites and respiration were more highly represented. Together, these novel insights provide a deeper understanding of highly diversified plant-specific light seed microbiota and ecological strategies for plants in harsh environments.

Reduced Colonic Mucosal Injury in 2,3,7,8-Tetrachlorodibenzo-p-Dioxin Poly ADP-Ribose Polymerase (TIPARP/PARP7)-Deficient Mice.

Poly-ADP-ribose polymerases (PARPs) are important regulators of the immune system, including TCDD-inducible poly-ADP-ribose polymerase (TIPARP), also known as poly-ADP-ribose polymerase 7 (PARP7). PARP7 negatively regulates aryl hydrocarbon receptor (AHR) and type I interferon (IFN-I) signaling, both of which have been implicated in intestinal homeostasis and immunity. Since the loss of PARP7 expression increases AHR and IFN-I signaling, we used a murine dextran sulfate sodium (DSS)-induced colitis model to investigate the effect of PARP7 loss on DSS-induced intestinal inflammation. DSS-exposed Parp7−/− mice had less body weight loss, lower disease index scores, and reduced expression of several inflammation genes, including interleukin IL-6, C-x-c motif chemokine ligand 1 (Cxcl1), and lipocalin-2, when compared with wild-type mice. However, no significant difference was observed between genotypes in the colonic expression of the AHR target gene cytochrome P450 1A1 (Cyp1a1). Moreover, no significant differences in microbial composition were observed between the genotypes. Our findings demonstrate that the absence of PARP7 protein results in an impaired immune response to colonic inflammation and suggests that PARP7 may participate in the recruitment of immune cells to the inflammation site, which may be due to its role in IFN-I signaling rather than AHR signaling.

The determination of skin surface pH via the skin volatile emission using wearable colorimetric sensors

Biodiagnostic sensors in the form of wearables have become of widespread interest in both the scientific and clinical communities in recent years due to their potential for monitoring human health, well-being and physical performance. However, collecting biofluids from the skin to enable biochemical analysis using wearables has proved challenging to date. This research seeks to overcome the need for fluid collection by designing a wearable sensing platform capable of monitoring the volatile emission from skin with the aim of collecting biodiagnostic information from the body. We investigate the use of a simple wearable colorimetric sensing platform incorporating sensor spots comprising encapsulated bromocresol green pH indicator dye in an enclosed headspace above the skin. The sensor spots undergo a colour change in response to basic volatile nitrogen compounds such as ammonia and amines being emitted from skin. By deploying this wearable in a healthy participant study, a strong correlation between sensor colour response and skin surface pH was demonstrated, despite a significant inter-individual variability being noted. Sensor response was observed to be highly dependent on gender as well as body site, and attributed to factors such as gland and microbial composition differences. Finally, the wearable's ability to detect changes in skin surface pH in response to topical skin treatments was demonstrated. Overall, this work demonstrates a novel and simple approach to wearable biodiagnostics that exploits the skin volatile emission to monitor skin physiology without the need for microneedles or the requirement to harvest fluid from the skin.

A Distinct Gut Microbial Ecology is Associated with Enhanced Chemosensitivity Following Neutrophil Attenuation in Pancreatic Cancer

Background: Infiltration of innate immune cells, such as neutrophils, in the tumor microenvironment (TME) are associated with worse oncologic outcomes in pancreatic ductal adenocarcinoma (PDAC). Given recent evidence highlighting the complex intersection between chemosensitivity and the gut microbiome in solid tumors, we sought to investigate if the enhanced chemosensitivity observed with neutrophil attenuation in PDAC is associated with a distinct gut microbial ecology. Methods: C57BL/6 mice were orthotopically injected with syngeneic KrasG12D/+;Trp53fl/+;Pdx-Cre(KPC) PDAC cells, and randomized into four treatment groups after 10d tumor growth (n=8-10/arm): vehicle-control, anti-Ly6G antibody treatment alone with neutrophil-attenuating—but not depleting—dosing (25 μg/dose) q3d, gemcitabine(100 mg/kg) and paclitaxel(10 mg/kg) qwk(G/P), and G/P+anti-Ly6G. Fecal samples from mice (n=3/group) were collected 10d after treatment and submitted for shotgun metagenomic sequencing. Results: Bray-Curtis principal coordinate analysis of microbial β-diversity revealed significant differences in microbial composition with neutrophil attenuation and chemotherapy. Abundance of 37 species were differentially significant between G/P+anti-Ly6G and G/P-treated cohorts (p-adj<0.05). Seven Alistipes spp. (class Bacteroidea)—previously associated with chemoresistance in solid cancers—were significantly reduced in the gut microbiome of G/P+anti-Ly6G-treated mice. Bifidobacterium pseudolongum, previously associated with PDAC tumor progression, was the most significantly reduced bacterial species in the gut microbiome of G/P+anti-Ly6G-treated mice when compared with G/P alone-group. Conclusion: Our data unearth potential crosstalk between a distinct but narrow gut microbial ecology and anti-tumor adaptive immunity in response to neutrophil attenuation that is associated with improved chemosensitivity in PDAC. Therapeutic manipulation of this microbial program may mitigate chemoresistance and improve outcomes in PDAC patients.

Breed and diet influence the ruminal bacterial community of sheep

Context Ruminal microbial communities are important in production ruminants, as they can affect health and production efficiency. Differences between meat- and wool-producing sheep breeds have not yet been fully explored. Aims In this study, we aimed to determine the impact of diet on ruminal microbial populations of sheep selected for different production traits, namely, meat production (White Suffolk) and wool production, and quality (Poll Merino). Methods The study utilised 24 White Suffolk and 24 Poll Merino ewes, assigned to either a roughage (20% pellet and 80% chaff) or high-grain diet (80% pellet and 20% chaff). Following acclimatisation for 21 days, they each had a ruminal sample taken and analysed for bacterial communities, using 16S rRNA sequencing. Entry and exit weight of the ewes and their feed intake were measured. Key results There was a preference for the high-grain diet (P &lt; 0.0001), with greater amounts consumed, although there was no significant difference in ewe weights between the two dietary treatments. However, White Suffolk ewes lost weight on the roughage diet, whereas all other groups gained weight (White Suffolk roughage −5.9 ± 2.6 kg, White Suffolk high-grain 7.8 ± 1.7 kg, Poll Merino roughage 9.2 ± 2.7 kg, Poll Merino high-grain 5.0 ± 1.8 kg). There were significant ruminal bacterial differences associated with both diet and breed. The average dissimilarity in ruminal bacterial phyla associated with diet was 14.13%, with the top 50% of phyla contributing to the dissimilarity being Verrucomicrobia, Lentisphaerae, Elusimicrobia, SR1 and Fibrobacteres, which were significantly more abundant in the roughage dietary group, and Proteobacteria, which were significantly more abundant in the high-grain dietary group. Conclusions We have demonstrated that although diet strongly influences the ruminal microbiota, there is a significant interaction between diet and breed in effects on ruminal microbiota and also animal performance. Implications The differences in microbial composition between breeds were related to some of the animal productivity differences of the two breeds, indicating that at least some of the genetic differences in animal productivity are generated by differences in the responsiveness of the ruminal microbiota to diet.

Soybean Roots and Soil From High- and Low-Yielding Field Sites Have Different Microbiome Composition.

The occurrence of high- (H) and low- (L) yielding field sites within a farm is a commonly observed phenomenon in soybean cultivation. Site topography, soil physical and chemical attributes, and soil/root-associated microbial composition can contribute to this phenomenon. In order to better understand the microbial dynamics associated with each site type (H/L), we collected bulk soil (BS), rhizosphere soil (RS), and soybean root (R) samples from historically high and low yield sites across eight Pennsylvania farms at V1 (first trifoliate) and R8 (maturity) soybean growth stages (SGS). We extracted DNA extracted from collected samples and performed high-throughput sequencing of PCR amplicons from both the fungal ITS and prokaryotic 16S rRNA gene regions. Sequences were then grouped into amplicon sequence variants (ASVs) and subjected to network analysis. Based on both ITS and 16S rRNA gene data, a greater network size and edges were observed for all sample types from H-sites compared to L-sites at both SGS. Network analysis suggested that the number of potential microbial interactions/associations were greater in samples from H-sites compared to L-sites. Diversity analyses indicated that site-type was not a main driver of alpha and beta diversity in soybean-associated microbial communities. L-sites contained a greater percentage of fungal phytopathogens (ex: Fusarium, Macrophomina, Septoria), while H-sites contained a greater percentage of mycoparasitic (ex: Trichoderma) and entomopathogenic (ex: Metarhizium) fungal genera. Furthermore, roots from H-sites possessed a greater percentage of Bradyrhizobium and genera known to contain plant growth promoting bacteria (ex: Flavobacterium, Duganella). Overall, our results revealed that there were differences in microbial composition in soil and roots from H- and L-sites across a variety of soybean farms. Based on our findings, we hypothesize that differences in microbial composition could have a causative relationship with observed within-farm variability in soybean yield.

Comparative analysis of human facial skin microbiome between topical sites compared to entire face.

Skin is an essential outer barrier and supports the growth of commensal microorganisms that protects a host from the offense of foreign toxic organisms. With the rapid development of next-generation sequencing (NGS)-based applications, skin microbiome research for facial health care has reached industry growth, such as therapy and cosmetic product development. Despite the acceleration of skin microbiome research, experimental standardization protocol has not yet been established in the facial site and method of sampling. Thus, we aimed to investigate the differences in microbial composition at each facial site (cheek, mouth, forehead, and entire face) using comprehensive microbiome analysis. Twelve specimens from three men (four specimens per one person) were collected. The hypervariable regions (V3-V4) of the bacterial 16S rRNA gene were targeted for 16S amplicon library construction and classification of bacterial taxonomy. Skin microbial composition for all specimens was investigated, and the differences site-by-site in skin microbial composition were analyzed and evaluated by the various statistical tests. We were able to validate the independent correlation between the skin microbiome composition and the facial sites. The cheek site showed the highest alpha-diversity in richness and evenness scores compared to the forehead and mouth. The cheek and mouth sites showed a positive correlation (R2 value > 0.93) with the entire face, while the forehead sites were negatively correlated (R2 value < 0.2). Given the relative abundance based on statistical correlation analysis, we estimated that the cheek site could be considered an optimal topical site to replace the entire face. Our study suggests that skin microbiome profiling of four facial sites confirms that the cheek shows the most similar skin flora with the entire face. This study would be informative for preventing bias caused by sampling methods before researching and understanding skin cosmetics development or skin diseases.

New insights to the difference in microbial composition and interspecies interactions between fouling layer and mixed liquor in a membrane bioreactor

This work examined fouling-associated microbial community in a carefully controlled laboratory-scale membrane bioreactor (MBR) at different fouling stages. In agreement with the literature, fouling severity was positively correlated with bound polysaccharide and protein content (indicators) in the mixed liquor. UPGMA clustering analysis with different indices indicated that although the biofouling layer (biofilm) and mixed liquor possessed highly similar microbial identity, important differences between the two communities' structures were also observed. This appears to be the first comprehensive study to apply differential abundance analysis (ANCOM) to identify microbial taxa driven the divergence in microbial structure including Victivallales, Coxiellales, unassigned Microgenomatia and Blastocatellia 11–24 (all presented at <1% abundance). Network analysis also identified Victivallales and Blastocatellia 11–24 among the few key players in the mixed liquor and biofilm community, respectively. Despite their low abundances, key players in both communities positively correlated (Pearson's correlation coefficient >0.6) with fouling indicators, confirming their important contributions to fouling propensity. The biofilm community exhibited a more complex structure with higher level of inter-species interaction and prevalence of positive connections (74.6%) compared to the mixed liquor community (42.2%), reflecting higher stability and synergy between microbial taxa in the biofilm. Results from this comprehensive investigation can support the development of new fouling control strategies.

Organic carbon composition and microbial transformation of seagrass meadow and its responses to eutrophication

<p indent="0mm">Carbon neutrality is an important concept in global climate change governance. Seagrass beds rank among the most productive autotrophic ecosystems on the planet, and are receiving increasing attention as globally-significant hotspots of organic carbon (“blue carbon”) sequestration. The blue carbon stored in seagrass beds has important implications for climate change mitigation. The protection of seagrass beds will also protect their organic carbon sequestration potential, consequently helping to achieve the goal of carbon neutrality. Unfortunately, about 29% of the world’s seagrass beds have been destroyed, with a loss rate of 7% a⁻¹ since 1990, mostly due to eutrophication. The organic carbon sequestration potential of seagrass beds could be influenced by the subsequent changes in organic carbon composition, and microbial transformation processes. We systematically reviewed the relevant local and international research to summarize the composition and microbial transformation of organic carbon and its responses to eutrophication. Organic carbon is present in various forms in seagrass beds, and can be roughly divided into primary producer living biomass carbon, litter organic carbon, water organic carbon, and sediment organic carbon according to its storage area. Organic carbon can also be divided into labile organic carbon (LOC), which is susceptible to microbial decomposition, and recalcitrant organic carbon (ROC), which is resistant to microbial decomposition. The total ROC (cellulose and lignin) content in seagrass is present in the range of <sc>153−561 mg/g,</sc> and accounts for more than 28.7% of the organic carbon in the seagrass plants. The ROC content of seagrass plants is affected by the species, morphology, tissue and organ types, and climatic zones. In the water column, color dissolved organic matter (CDOM) and neutral sugars are indicators of LOC, while the lignin phenol and humic-like fractions of fluorescent dissolved organic matter (FDOM) are potential tracers of ROC. The DOM in water can be divided into dissolved organic carbon (DOC), dissolved organic nitrogen (DON), and dissolved organic phosphorus (DOP). The DOC/DON and DOC/DOP ratios are used to reflect DOC lability and microbial bioavailability, with high DON and DOP concentrations indicating high DOC lability. In sediments, extractable organic carbon and microbial biomass carbon are important indicators of LOC, while aromatic hydrocarbons and alkanes are indicative of recalcitrant components. There are significant differences in the sediment organic carbon contents of temperate and tropical regions. Microorganisms play a vital role in the transformation of organic carbon. There are geographic differences in microbial composition, which are mainly influenced by the available habitats and climate zones, but there are no differences between seagrass species within a fine-scale seagrass bed. Different microorganisms have different decomposition capacities. <italic>R</italic>-strategist microbes, including Clostridiales<italic> </italic>and<italic> </italic>Gammaproteobacteria, are able to rapidly decompose LOC, while <italic>k</italic>-strategists, such as Verrucomicrobiae<italic> </italic>and Anaerolinae, can break down the more recalcitrant compounds. There is a succession of <italic>r</italic>- to <italic>k</italic>-strategists microbes during the decomposition of fresh organic matter (including fresh seagrass litter, DOC, and SOC). Eutrophication may lead to the transformation of the community structure of primary producers in seagrass beds from seagrass to macroalgae, which will increase the input of labile carbon. This consequently causes an increase in LOC in the plant biomass, water column, and sediments, but a decrease in ROC. The nutrient loading can affect the microbial community structure and enzyme activity, which will affect the microbial transformation of organic carbon. Furthermore, nutrient and LOC inputs may induce a “priming effect” that promotes the remineralization of stored organic carbon. Several future research directions for determining the transformation of seagrass beds and their organic carbon were proposed. (1) Extensive studies of the organic carbon components (LOC and ROC) in seagrass beds are required. (2) There is a need to better understand the composition, function, and gene expression of microbial communities in seagrass beds. (3) The eutrophication mechanisms in microbial communities and the related extracellular enzyme activities need to be determined. (4) The response of the organic matter decomposition process to nutrient loading and the interaction of nutrients and algae need to be studied. There is also a need to strengthen local research on the carbon storage potential of seagrass beds to mitigate global climate change and provide theoretical support for achieving carbon neutrality.

Effects of Long-Term Triclosan Exposure on Microbiota in Zebrafish.

Background: Triclosan (TCS) is a widely used antibacterial agent in personal care products and is ubiquitous in the environment. We aimed to examine whether TCS exposure affects microbiota in the gastrointestinal tract of zebrafish.Methods: After exposure to TCS 0 (Dimethyl Sulphoxide, DMSO control), 0.03, 0.3, 3, 30, 100, and 300ng/ml, respectively, from day 0 to 120days post fertilization (dpf), or for 7days in adult 4-month zebrafish, the long- and short-term impact of TCS exposure on the microbiome in the gastrointestinal tract was evaluated by analyzing 16S rRNA gene V3-V4 region sequencing.Results: The top two most dominant microbiota phyla were Proteobacteria and Fusobacteria phylum in all zebrafish groups. In TCS exposure 0–120 dpf, compared with DMSO control, the mean number of microbial operational taxonomic units (OTUs) was 54.46 lower (p<0.0001), Chao indice 41.40 lower (p=0.0004), and Ace indice 34.10 lower (p=0.0044) in TCS 300ng/ml group, but no change was observed in most of the other TCS concentrations. PCoA diagram showed that the microbial community in the long-term TCS 300ng/ml exposure group clustered differently from those in the DMSO control and other TCS exposure groups. A shorter body length of the zebrafish was observed in the long-term TCS exposure at 0.03, 100, and 300ng/ml. For 7-day short-term exposure in adult zebrafish, no difference was observed in alpha or beta diversity of microbiota nor the relative abundance of Proteobacteria or Fusobacteria phylum among DMSO control and any TCS levels, but a minor difference in microbial composition was observed for TCS exposure.Conclusions: Long-term exposure to high TCS concentration in a window from early embryonic life to early adulthood may reduce diversity and alter the composition of microbiota in the gastrointestinal tract. The effect of short-term TCS exposure was not observed on the diversity of microbiota but there was a minor change of microbial composition in adult zebrafish with TCS exposure.

In vitro Prebiotic Effect of Bread-Making Process in Inflammatory Bowel Disease Microbiome.

Inflammatory bowel disease (IBD), including its two main categories (Crohn's disease and ulcerative colitis), has been linked both to gut microbiota and to diet. Bread is a daily food that has a potential capacity as a prebiotic. Our aim was to evaluate different bread-making processes and their effect on fecal colonic microbiota in IBD patients. The microbial composition of several sourdoughs and dough samples was analyzed by high-throughput sequencing of 16S and 18S rRNA genes. Three types of bread, which followed different bread-making processes, were in vitro digested and incubated with feces from IBD patients. Changes in gut microbiota were assessed by a quantitative polymerase chain reaction using specific bacterial sequence targets. Short-chain fatty acid production was also analyzed by gas chromatography. Lactobacillus sanfranciscensis was the dominant lactic acid bacteria species found in sourdough and bread doughs prepared using sourdough, whereas Saccharomyces cerevisiae was the most dominant yeast in all groups, especially in bread doughs before baking. Differences in microbial composition in raw bread doughs were more related to the type of dough and elaboration than to fermentation time lengths. The analysis of in vitro fecal incubations with bread conditions revealed an increase in most bacterial groups analyzed and short-chain fatty acid production, both in Crohn's disease and ulcerative colitis samples. Most remarkable increases in short-chain fatty acid production mirrored higher abundances of Roseburia species. The potential prebiotic properties observed were mainly obtained when using a high quantity of bread, regardless of bread type. Overall, this study highlights the bacterial dynamics within the bread-making process and the potential prebiotic effect in IBD patients.

The Lung Microbiome during Health and Disease

Healthy human lungs have traditionally been considered to be a sterile organ. However, culture-independent molecular techniques have reported that large numbers of microbes coexist in the lung and airways. The lungs harbor diverse microbial composition that are undetected by previous approaches. Many studies have found significant differences in microbial composition between during health and respiratory disease. The lung microbiome is likely to not only influence susceptibility or causes of diseases but be affected by disease activities or responses to treatment. Although lung microbiome research has some limitations from study design to reporting, it can add further dimensionality to host-microbe interactions. Moreover, there is a possibility that extending understanding to the lung microbiome with new multiple omics approaches would be useful for developing both diagnostic and prognostic biomarkers for respiratory diseases in clinical settings.

Differences in the Oral Microbiome in Patients With Early Rheumatoid Arthritis and Individuals at Risk of Rheumatoid Arthritis Compared to Healthy Individuals.

ObjectiveIt has been suggested that rheumatoid arthritis (RA) may originate at the oral mucosa. The aim of the present study was to assess the oral microbiome and periodontal condition in patients with early RA and individuals at risk of developing RA compared to healthy controls.MethodsThree groups were recruited (n = 50 participants per group): 1) patients with early RA (meeting the American College of Rheumatology/European Alliance of Associations for Rheumatology 2010 classification criteria), 2) individuals at risk of developing RA (those with arthralgia who were positive for RA‐associated autoantibodies), and 3) healthy controls. A periodontal examination was conducted to assess the presence of bleeding on probing (BOP), pocket probing depth (PPD), and periodontal inflamed surface area (PISA). The microbial composition of subgingival dental plaque, saliva, and tongue coating was assessed using 16S ribosomal DNA amplicon sequencing, and findings were compared between groups with permutational multivariate analysis of variance (PERMANOVA).ResultsThere were no significant differences in any of the 3 periodontal variables between patients with early RA, at‐risk individuals, and healthy controls (P = 0.70 for BOP, P = 0.30 for PPD, and P = 0.57 for PISA, by Kruskal‐Wallis test). PERMANOVA analyses comparing microbial composition between the groups showed significant differences in the microbial composition of saliva (F = 2.08, P = 0.0002) and tongue coating (F = 2.04, P = 0.008), but not subgingival dental plaque (F = 0.948, P = 0.51). However, in post hoc tests, no significant differences in microbial composition of the saliva or tongue coating were observed between the early RA group and the at‐risk group (F = 1.12, P = 0.28 for saliva; F = 0.834, P = 0.59 for tongue coating). In assessing microbial diversity based on the number of zero‐radius operational taxonomic units per sample, Prevotella in the saliva and Veillonella in the saliva and tongue coating were each found at a higher relative abundance in samples from patients with early RA and at‐risk individuals compared to healthy controls.ConclusionThe results show similarities in the oral microbiome between patients with early RA and at‐risk individuals, since in both groups, the oral microbiome was characterized by an increased relative abundance of potentially proinflammatory species when compared to that in healthy controls. These findings suggest a possible association between the oral microbiome and the onset of RA.