Search

Objectives. Microorganisms are likely present in continuous positive airway pressure (CPAP) devices in daily use. Given the potential risk of infection among CPAP users, we aimed to compare the microbiomes of CPAP devices with those of nasal mucosa samples obtained from patients using these devices. Methods. We conducted a prospective cohort study at multiple tertiary medical institutions. Samples were collected from the tubes and filters of CPAP devices and the nasal mucosa of device users. Microbiomes and mycobiomes were analyzed using 16S ribosomal RNA and internal transcribed spacer region sequencing. The results were compared according to sampling site and usage duration for each patient. Results. Overall, 27 paired samples of human nasal mucosa and CPAP components were analyzed. Bacteria were detected in 7 of the 27 tubes (25.9%) and in 22 of the 27 filters (81.5%). Fungi were found in 2 tubes (7.4%) and 16 filters (59.3%). The most prevalent bacterial phyla across all samples were Actinobacteria and Firmicutes. Fungi were not detected in any nasal mucosa samples. However, fungi were identified in the CPAP filters and tubes, with the Basidiomycota and Ascomycota phyla predominating. No significant associations were identified according to sampling site or duration of CPAP use. Conclusion. Some bacteria or fungi are detectable in CPAP samples, even after a short period of CPAP usage. However, the association between respiratory infections and these microbiomes or mycobiomes was not investigated. Further research is required to clarify the risk posed by CPAP devices as a microbial contamination source.

Abstract Geothermal features in Antarctica provide favorable conditions for diverse microorganisms, yet their genomic diversity remains poorly understood. Here, we present an integrated dataset comprising PacBio HiFi and Hi-C metagenomic sequencing, along with single-cell amplified genomes (SAGs) from two high-altitude geothermal sites, Mount Melbourne and Mount Rittmann, in Antarctica. The long-read HiFi sequencing, coupled with Hi-C, enhances the understanding of microbiome diversity and functionality in this unique ecosystem by providing more complete and accurate genomic information. SAGs complement this by recovering rare microbial taxa and offering a strain-resolved perspective. This dataset aims to deepen our understanding of microbial evolution and ecology in Antarctic geothermal environments, and facilitate cross-comparison with other geothermal environments globally.

Abstract The mariculture industry has seen a rapid expansion in recent years due to the increasing global demand for seafood. However, the industry faces challenges from climate change and increased pathogen pressure. Additionally, the chemicals used to enhance mariculture productivity are changing ocean ecosystems. This study analyzed 36 surface-water metagenomes from South Korean mussel, oyster, scallop, and shrimp farms to expand our understanding of aquaculture microbial genetic resources and the potential impacts of these anthropogenic inputs. We recovered 240 non-redundant species-level metagenome-assembled genomes (MAGs), comprising 224 bacteria, 13 archaea, and three eukaryotes. Most MAGs were assigned to Proteobacteria, Bacteroidota, and Actinobacteriota, with 40.7% remaining unclassified at the species level. Among the three eukaryotic MAGs, one was identified as a novel lineage of green algae, highlighting the uncharacterized genetic diversity in mariculture environments. Additionally, 22 prokaryotic MAGs harbored 26 antibiotic and metal resistance genes, with MAGs carrying beta-lactamases being particularly prevalent in most farms. The obtained microbiome data from mariculture environments can be utilized in future studies to foster healthy, sustainable mariculture practices.

Abstract Background While significant research exists on gut microbiota changes after anti-tumor necrosis factor-alpha (anti TNF-α) therapy for ulcerative colitis, little is known about the longitudinal changes related to the effects of anti TNF-α. This study aimed to investigate the dynamics of gut microbiome changes during anti TNF-α (adalimumab) therapy in patients with ulcerative colitis (UC). Results The microbiota composition was affected by the disease severity and extent in patients with UC. Regardless of clinical remission status at each time point, patients with UC exhibited microbial community distinctions from healthy controls. Distinct amplicon sequence variants (ASVs) differences were identified throughout the course of Adalimumab (ADA) treatment at each time point. A notable reduction in gut microbiome dissimilarity was observed only in remitters. Remitters demonstrated a decrease in the relative abundances of Burkholderia-Caballeronia-Paraburkholderia and Staphylococcus as the treatment progressed. Additionally, there was an observed increase in the relative abundances of Bifidobacterium and Dorea. Given the distribution of the 48 ASVs with high or low relative abundances in the pre-treatment samples according to clinical remission at week 8, a clinical remission at week 8 with a sensitivity and specificity of 72.4% and 84.3%, respectively, was predicted on the receiver operating characteristic curve (area under the curve, 0.851). Conclusions The gut microbiota undergoes diverse changes according to the treatment response during ADA treatment. These changes provide insights into predicting treatment responses to ADA and offer new therapeutic targets for UC.

Abstract This study aims to characterize levels of molds, bacteria, and environmental pollutants, identify the associations between indoor mold and dampness exposures and childhood allergic diseases, including asthma, allergic rhinitis, atopic dermatitis, using three different exposure assessment tools. A total of 50 children with their parents who registered in Seoul and Gyeonggi-do in Korea participated in this study. We collated the information on demographic and housing characteristics, environmental conditions, and lifestyle factors using the Korean version of the International Study of Asthma and Allergies in Childhood questionnaire. We also collected environmental monitoring samples of airborne molds and bacteria, total volatile organic compounds, formaldehyde, and particulate matter less than 10 µm. We evaluated and determined water damage, hidden dampness, and mold growth in dwellings using an infrared (IR) thermal camera and field inspection. Univariate and multivariate regression analyses were performed to evaluate the associations between prevalent allergic diseases and exposure to indoor mold and dampness. Indoor mold and bacterial levels were related to the presence of water damage in dwellings, and the mean levels of indoor molds (93.4 ± 73.5 CFU/m3) and bacteria (221.5 ± 124.2 CFU/m3) in water-damaged homes were significantly higher than those for molds (82.0 ± 58.7 CFU/m3) and for bacteria (152.7 ± 82.1 CFU/m3) in non-damaged dwellings (p

Abstract The interaction between the microbial environment and the host is important for immune homeostasis. Recent research suggests that microbiota dysbiosis can be involved in respiratory diseases. Emphysema is a chronic inflammatory disease, but it is unclear whether dysbiosis caused by antibiotics can affect disease progression. Here, we tried to elucidate the effect of systemic antibiotics on smoking-exposed emphysema models. In this study, the antibiotic mixture caused more alveolar destruction and airspace expansion in the smoking group than in the smoking only or control groups. This emphysema aggravation as a result of antibiotic exposure was associated with increased levels of inflammatory cells, IL-6, IFNγ and protein concentrations in bronchoalveolar lavage fluid. Proteomics analysis indicated that autophagy could be involved in antibiotic-associated emphysema aggravation, and increased protein levels of LC3B, atg3, and atg7 were identified by Western blotting. In microbiome and metabolome analyses, the composition of the gut microbiota was different with smoking and antibiotic exposure, and the levels of short-chain fatty acids (SCFAs), including acetate and propionate, were reduced by antibiotic exposure. SCFA administration restored emphysema development with reduced inflammatory cells, IL-6, and IFNγ and decreased LC3B, atg3, and atg7 levels. In conclusion, antibiotics can aggravate emphysema, and inflammation and autophagy may be associated with this aggravation. This study provides important insight into the systemic impact of microbial dysbiosis and the therapeutic potential of utilizing the gut microbiota in emphysema.

Candidate strains that contribute to drought resistance in plants have been previously screened using approximately 500 plant growth-promoting rhizobacteria (PGPR) obtained from Gotjawal, South Korea, to further understand PGPR associated with plant drought tolerance. In this study, a selected PGPR candidate, Flavobacterium sp. strain GJW24, was employed to enhance plant drought tolerance. GJW24 application to Arabidopsis increased its survival rate under drought stress and enhanced stomatal closure. Furthermore, GJW24 promoted Arabidopsis survival under salt stress, which is highly associated with drought stress. GJW24 ameliorated the drought/salt tolerance of Brassica as well as Arabidopsis, indicating that the drought-resistance characteristics of GJW24 could be applied to various plant species. Transcriptome sequencing revealed that GJW24 upregulated a large portion of drought- and drought-related stress-inducible genes in Arabidopsis. Moreover, Gene Ontology analysis revealed that GJW24-upregulated genes were highly related to the categories involved in root system architecture and development, which are connected to amelioration of plant drought resistance. The hyper-induction of many drought/salt-responsive genes by GJW24 in Arabidopsis and Brassica demonstrated that the drought/salt stress tolerance conferred by GJW24 might be achieved, at least in part, through regulating the expression of the corresponding genes. This study suggests that GJW24 can be utilized as a microbial agent to offset the detrimental effects of drought stress in plants.

Abstract Background DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in culturable microorganisms, resulting in a limited understanding of DNA methylation from a microbial ecology perspective. Here, we analyze the distribution patterns of several microbial epigenetics marks in the ocean microbiome through genome-centric metagenomics across all domains of life. Results We reconstructed 15,056 viral, 252 prokaryotic, 56 giant viral, and 6 eukaryotic metagenome-assembled genomes from northwest Pacific Ocean seawater samples using short- and long-read sequencing approaches. These metagenome-derived genomes mostly represented novel taxa, and recruited a majority of reads. Thanks to single-molecule real-time (SMRT) sequencing technology, base modification could also be detected for these genomes. This showed that DNA methylation can readily be detected across dominant oceanic bacterial, archaeal, and viral populations, and microbial epigenetic changes correlate with population differentiation. Furthermore, our genome-wide epigenetic analysis of Pelagibacter suggests that GANTC, a DNA methyltransferase target motif, is related to the cell cycle and is affected by environmental conditions. Yet, the presence of this motif also partitions the phylogeny of the Pelagibacter phages, possibly hinting at a competitive co-evolutionary history and multiple effects of a single methylation mark. Conclusions Overall, this study elucidates that DNA methylation patterns are associated with ecological changes and virus-host dynamics in the ocean microbiome. Video Abstract

Abstract We examined differences in the skin microbiome of two separate age groups to find key microbial and skin physiological indicators associated with aging. We recruited healthy Korean women 19–28 years old (Y-group) and 60–63 years old (O-group) and evaluated their cheek and forehead skin microbiome, including bacteria and fungi. The microbiome was significantly different by age group, with bacterial and fungal communities displaying higher alpha-diversity in the O-group than in the Y-group. We identified amplicon sequence variants affiliated with Cutibacterium and Lactobacillus and fungi Malassezia restricta as microbial biomarkers showing significant differences between the Y and O-group. There are more microbial communities and metabolic processes related to skin health in the Y-group than in the O-group, and there are more microbial interactions to increase the stability of the network structure of the skin. Skin physical metadata, including transepidermal water loss and sebum content, differed by two age groups. The crucial skin microbes, skin physical parameters, and microbial network found through this research will be useful key indicators in associating skin aging and skin microbiome research.

ABSTRACT Malassezia is a fungal genus found on the skin of humans and warm-blooded animals, with 18 species reported to date. In this study, we sequenced and annotated the genome of Malassezia arunalokei, which is the most recently identified Malassezia species, and compared it with Malassezia restricta, the predominant isolate from human skin. Additionally, we reanalyzed previously reported mycobiome data sets with a species-level resolution to investigate M. arunalokei distribution within the mycobiota of human facial skin. We discovered that the M. arunalokei genome is 7.24 Mbp in size and encodes 4,117 protein-coding genes, all of which were clustered with M. restricta. We also found that the average nucleotide identity value of the M. arunalokei genome was 93.5, compared with the genomes of three M. restricta strains, including M. restricta KCTC 27527. Our findings demonstrate that they indeed belong to different species and that M. arunalokei may have experienced specific gene loss events during speciation. Furthermore, our study showed that M. arunalokei was diverged from M. restricta approximately 7.1 million years ago and indicated that M. arunalokei is the most recently diverged species in the Malassezia lineage to date. Finally, our analysis of the facial mycobiome of previously recruited cohorts revealed that M. arunalokei abundance is not associated with seborrheic dermatitis/dandruff or acne, but was revealed to be more abundant on the forehead and cheek than on the scalp. IMPORTANCE Malassezia is the fungus predominantly residing on the human skin and causes various skin diseases, including seborrheic dermatitis and dandruff. To date, 18 species have been reported, and among them, M. restricta is the most predominant on human skin, especially on the scalp. In this study, we sequenced and analyzed the genome of M. arunalokei, which is the most recently identified Malassezia species, and compared it with M. restricta. Moreover, we analyzed the fungal microbiome to investigate the M. arunalokei distribution on human facial skin. We found that M. arunalokei may have experienced specific gene loss events during speciation. Our study also showed that M. arunalokei was diverged from M. restricta approximately 7.1 million years ago and indicated that M. arunalokei is the most recently diverged species in the Malassezia lineage. Finally, our analysis of the facial mycobiome revealed that M. arunalokei has higher relative abundance on the forehead and cheek than the scalp.

Hundreds of tons of antibiotics are widely used in aquaculture to prevent microbial infections and promote fish growth. However, the overuse of antibiotics and chemical products can lead to the selection and spreading of antibiotic-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs), which are of great concern considering the threat to public health worldwide. Here, in-depth metagenome sequencing was performed to explore the environmental resistome and ARB distribution across farming stages in shrimp farms and examine anthropogenic effects in nearby coastal waters. A genome-centric analysis using a metagenome binning approach allowed us to accurately investigate the distribution of pathogens and ARG hosts in shrimp farms. The diversity of resistomes was higher in shrimp farms than in coastal waters, and the distribution of resistomes was dependent on the farming stage. In particular, the tetracycline resistance gene was found mainly at the early post-larval stage regardless of the farm. The metagenome-assembled genomes of Vibrio spp. were dominant at this stage and harbored tet34, which is known to confer resistance to oxytetracycline. In addition, opportunistic pathogens such as Francisella, Mycoplasma, Photobacterium, and Vibrio were found in abundance in shrimp farms, which had multiple virulence factors. This study highlights the increased resistance diversity and environmental selection of pathogens in shrimp farms. The use of environmental pollutants on farms may cause an increase in resistome diversity/abundance and the transmission of pathogens to the surrounding environment, which may pose future risks to public health and aquatic organisms.

Abstract Background The impact of human activities on the environmental resistome has been documented in many studies, but there remains the controversial question of whether the increased antibiotic resistance observed in anthropogenically impacted environments is just a result of contamination by resistant fecal microbes or is mediated by indigenous environmental organisms. Here, to determine exactly how anthropogenic influences shape the environmental resistome, we resolved the microbiome, resistome, and mobilome of the planktonic microbial communities along a single river, the Han, which spans a gradient of human activities. Results The bloom of antibiotic resistance genes (ARGs) was evident in the downstream regions and distinct successional dynamics of the river resistome occurred across the spatial continuum. We identified a number of widespread ARG sequences shared between the river, human gut, and pathogenic bacteria. These human-related ARGs were largely associated with mobile genetic elements rather than particular gut taxa and mainly responsible for anthropogenically driven bloom of the downstream river resistome. Furthermore, both sequence- and phenotype-based analyses revealed environmental relatives of clinically important proteobacteria as major carriers of these ARGs. Conclusions Our results demonstrate a more nuanced view of the impact of anthropogenic activities on the river resistome: fecal contamination is present and allows the transmission of ARGs to the environmental resistome, but these mobile genes rather than resistant fecal bacteria proliferate in environmental relatives of their original hosts. Video abstract.

Objective As laying hens become aged, laying performance and egg quality are generally impaired. One of the practical methods to rejuvenate production and egg quality of aged laying hens with decreasing productivity is a forced molting. However, the changes in intestinal microbiota after forced molting of aged hens are not clearly known. The aim of the present study was to analyze the changes in excreta bacterial communities after forced molting of aged laying hens. Methods A total of one hundred 66-wk-old Hy-Line Brown laying hens were induced to molt by a 2-d water removal and an 11-d fasting until egg production completely ceased. The excreta samples of 16 hens with similar body weight were collected before and immediately after molting. Excreta bacterial communities were analyzed by high-throughput sequencing of bacterial 16S rRNA genes. Results Bacteroidetes, Firmicutes, and Proteobacteria were the three major bacterial phyla in pre-molting and immediate post-molting hens, accounting for more than 98.0%. Lactobacillus genus had relatively high abundance in both group, but decreased by molting (62.3% in pre-molting and 24.9% in post-molting hens). Moreover, pathogenic bacteria such as Enterococcus cecorum and Escherichia coli were more abundant in immediate post-molting hens than in pre-molting hens. Forced molting influenced the alpha diversity, with higher Chao1 (p = 0.012), phylogenetic diversity whole tree (p = 0.014), observed operational taxonomic unit indices (p = 0.006), and Simpson indices (p

ABSTRACT Neonatal calf diarrhea is a common disease leading to a major economic loss for cattle producers worldwide. Several infectious and noninfectious factors are implicated in calf diarrhea, but disease control remains problematic because of the multifactorial etiology of the disease. Here, we conducted diagnostic multiplex PCR assay and meta-omics analysis (16S rRNA gene-based metataxonomics and untargeted transcriptional profiling) of rectal content of normal and diarrheic beef calves (n = 111). In the diarrheic calf gut, we detected both microbial compositional dysbiosis (i.e., increased abundances of the family Enterobacteriaceae members and their lytic bacteriophages) and functional dysbiosis (i.e., elevated levels of aerobic respiration and virulence potential). The calf diarrheic transcriptome mirrored the gene expression of the bovine host and was enriched in cellular pathways of sulfur metabolism, innate immunity, and gut motility. We then isolated 12 nontoxigenic Enterobacteriaceae strains from the gut of diarrheic calves. Feeding a strain mixture to preweaning mice resulted in a significantly higher level of fecal moisture content, with decreased body weight gain and shortened colon length. The presented findings suggest that gut inflammation followed by a prolonged expansion of nontoxigenic autochthonous Enterobacteriaceae contributes to the onset of diarrhea in preweaning animals. IMPORTANCE Calf diarrhea is the leading cause of death of neonatal calves worldwide. Several infectious and noninfectious factors are implicated in calf diarrhea, but disease control remains problematic because of the multifactorial etiology of the disease. The major finding of the current study centers around the observation of microbial compositional and functional dysbiosis in rectal samples from diarrheic calves. These results highlight the notion that gut inflammation followed by a prolonged expansion of autochthonous Enterobacteriaceae contributes to the onset of calf diarrhea. Moreover, this condition possibly potentiates the risk of invasion of notorious enteric pathogens, including Salmonella spp., and the emergence of inflammation-resistant (or antibiotic-resistant) microbiota via active horizontal gene transfer mediated by lytic bacteriophages.

Bacterial contamination of food-contact surfaces can be a potential risk factor for food quality and safety. To evaluate the spatial and temporal variations of the potential cross-contamination routes, we conducted a biogeographical assessment of bacteria in a foodservice facility based on the diversity of microflora on each surface. To this end, we performed high-throughput amplicon sequencing of 13 food-contact and non-food contact surfaces in a foodservice facility throughout a year. The results showed that Bacillus, Acinetobacter, Streptophyta, Enterobacter, Pseudomonas, Serratia, Enhydrobacter, Staphylococcus, Paracoccus, and Lysinibacillus were the dominant genera found on the kitchen surfaces of the foodservice facility. Depending on the season, changes in Firmicute/Proteobacteria ratios were observed, and the fan becomes the main source of outdoor air contamination. The microbial flow associated with spoilage was also observed throughout food preparation. Taken together, our results would be a powerful reference to hygiene managers for improvement of food processes.

Xanthomonas euvesicatoria (Xe) is a gram-negative phytopathogenic bacterium that causes bacterial spot disease in tomato/pepper leading to economic losses in plantations. DNA methyltransferases (MTases) are critical for the survival of prokaryotes; however, their functions in phytopathogenic bacteria remain unclear. In this study, we characterized the functions of two putative DNA MTases, XvDMT1 and XvDMT2, in Xe by generating XvDMT1- and XvDMT2-overexpressing strains, Xe(XvDMT1) and Xe(XvDMT2), respectively. Virulence of Xe(XvDMT2), but not Xe(XvDMT1), on tomato was dramatically reduced. To postulate the biological processes involving XvDMTs, we performed a label-free shotgun comparative proteomic analysis, and results suggest that XvDMT1 and XvDMT2 have distinct roles in Xe. We further characterized the functions of XvDMTs using diverse phenotypic assays. Notably, both Xe(XvDMT1) and Xe(XvDMT2) showed growth retardation in the presence of sucrose and fructose as the sole carbon source, with Xe(XvDMT2) being the most severely affected. In addition, biofilm formation and production of exopolysaccharides were declined in Xe(XvDMT2), but not Xe(XvDMT1). Xe(XvDMT2) was more tolerant to EtOH than Xe(XvDMT1), which had enhanced tolerance to sorbitol but decreased tolerance to polymyxin B. Using single-molecule real-time sequencing and methylation-sensitive restriction enzymes, we successfully predicted putative motifs methylated by XvDMT1 and XvDMT2, which are previously uncharacterized 6mA and 5mC DNA MTases, respectively. This study provided new insights into the biological functions of DNA MTases in prokaryotic organisms.

Background: Acid Blue 113 (AB113) is a typical azo dye, and the resulting wastewater is toxic and difficult to remove. Methods: The experimental culture was set up for the biodegradation of the azo dye AB113, and the cell growth and dye decolorization were monitored. Transcriptome sequencing was performed in the presence and absence of AB113 treatment. The key pathways and enzymes involved in AB113 degradation were found through pathway analysis and enrichment software (GO, EggNog and KEGG). Results: S. melonis B-2 achieved more than 80% decolorization within 24 h (50 and 100 mg/L dye). There was a positive relationship between cell growth and the azo dye degradation rate. The expression level of enzymes involved in benzoate and naphthalene degradation pathways (NADH quinone oxidoreductase, N-acetyltransferase and aromatic ring-hydroxylating dioxygenase) increased significantly after the treatment of AB113. Conclusions: Benzoate and naphthalene degradation pathways were the key pathways for AB113 degradation. NADH quinone oxidoreductase, N-acetyltransferase, aromatic ring-hydroxylating dioxygenase and CYP450 were the key enzymes for AB113 degradation. This study provides evidence for the process of AB113 biodegradation at the molecular and biochemical level that will be useful in monitoring the dye wastewater treatment process at the full-scale treatment.

Using a high-throughput metagenomic approach, we evaluated nifH-harboring bacterial communities and their assembly in the Gotjawal forest, which was naturally formed on basalt rocks with thin layer of soil. Significant differences in soil properties and community structure were observed in comparison with similar communities in various habitats, including other lava-formed forests (on Jeju Island and in Hawaii) and in regions with high humidity (Florida) or low temperatures (Alaska). nifH-harboring bacterial communities were found to assemble along gradients of environmental factors, particularly cation-exchange capacity. Unlike in other regions, in the Gotjawal forest, Paenibacillus and Clostridium, which belong to the phylum Firmicutes, were present in significantly higher proportion than in other regions. Network analysis suggested that much fewer co-occurrence relationships occurred in the Gotjawal forest than in other lava-formed forests. Our results indicate that the unique nifH-harboring bacterial community and its assembly in the Gotjawal forest are due to its distinctive soil properties, which has implications for microbial interactions and functional potentials.

Single-molecule real-time (SMRT) sequencing allows identification of methylated DNA bases and methylation patterns/motifs at the genome level. Using SMRT sequencing, diverse bacterial methylomes including those of Helicobacter pylori, Lactobacillus spp., and Escherichia coli have been determined, and previously unreported DNA methylation motifs have been identified. However, the methylomes of Xanthomonas species, which belong to the most important plant pathogenic bacterial genus, have not been documented. Here, we report the methylomes of Xanthomonas axonopodis pv. glycines (Xag) strain 8ra and X. campestris pv. vesicatoria (Xcv) strain 85-10. We identified N⁶-methyladenine (6mA) and N⁴-methylcytosine (4mC) modification in both genomes. In addition, we assigned putative DNA methylation motifs including previously unreported methylation motifs via REBASE and MotifMaker, and compared methylation patterns in both species. Although Xag and Xcv belong to the same genus, their methylation patterns were dramatically different. The number of 4mC DNA bases in Xag (66,682) was significantly higher (29 fold) than in Xcv (2,321). In contrast, the number of 6mA DNA bases (4,147) in Xag was comparable to the number in Xcv (5,491). Strikingly, there were no common or shared motifs in the 10 most frequently methylated motifs of both strains, indicating they possess unique species- or strain-specific methylation motifs. Among the 20 most frequent motifs from both strains, for 9 motifs at least 1% of the methylated bases were located in putative promoter regions. Methylome analysis by SMRT sequencing technology is the first step toward understanding the biology and functions of DNA methylation in this genus.

(1) Background: Dental calculus works as a niche wherein pathogenic bacteria proliferate in the oral cavity. Previous studies revealed the anticalculus activity of pyrophosphates, however there was no clinical study that evaluated microbiome changes associated with calculus inhibition. Therefore, the aim of this randomized clinical trial was to evaluate the calculus inhibition of pyrophosphate-containing toothpaste and its effect on oral microbiome changes. (2) Methods: Eighty subjects with a calculus index ≥2 on the lingual of the mandibular anterior tooth were randomly allocated to the test group that pyrophosphate-containing toothpaste was given to or the placebo control group. Full mouth debridement and standardized tooth brushing instruction were given before the allocation. Plaque index, gingival index, calculus index, probing depth, and bleeding on probing were measured at the baseline, and at 4, 8 and 12 weeks. Genomic DNA was extracted from the plaque samples collected at the baseline and at 12 weeks, and 16S ribosomal RNA gene amplicon sequencing was applied for microbiome analysis. (3) Results: None of the clinical parameters showed significant differences by visits or groups, except the plaque index of the test group, which reduced significantly between 4 and 12 weeks. A significant difference of microbiome between the baseline and 12 weeks was observed in the test group. Between baseline and 12 weeks, the proportion of Spirochetes decreased in the control group, and the proportions of Proteobacteria, Fusobacteria and Spirochetes in the phylum level and the proportions of Haemophilus, Fusobacterium and Capnocytophaga in the genus level decreased in the test group. In the test group, as plaque index decreased, Streptococcus increased, and Fusobacterium and Haemophilus parainfluenza decreased. (4) Conclusion: The use of pyrophosphate-containing toothpaste effectively inhibited the dysbiosis of the oral microbiome and the proliferation of pathogenic species in periodontal disease. Clinically, plaque formation in the pyrophosphate-containing toothpaste group was effectively decreased, however there was no significant change in calculus deposition.

Sensitive skin (SS) syndrome is a globally widespread, self-diagnosed discomfort characterized by subjective complaints. Although the skin microbiome is considered important in skin health, the relationship between the skin microbiome and skin sensitivity is still unknown. Here, we aimed to (i) investigate whether the microbiome and mycobiome of SS are distinct from those of non-sensitive skin (NS), and (ii) define the characteristics of the skin microbiome associated with skin sensitivity. A total of 42 Korean women subjects were recruited (SS, n = 23; NS, n = 19) and the microbiome/mycobiome of their right facial cheeks were analyzed. We identified the differential microbiome and mycobiome structures between SS and NS. The mycobiome of SS was more phylogenetically diverse than that of NS. Lactobacillus and Mucor racemosus were more abundant on SS than NS, whereas Malassezia restricta was less abundant. Interestingly, both skin microbiome and mycobiome varied according to the perceived skin sensitivities of the subjects. This study suggests that the skin microbiome and mycobiome are associated with skin sensitivity. Accordingly, it lays the foundation for developing microbiome-based cosmetics or remedies for individuals suffering from SS syndrome.

Chicken is a major food source for humans, hence it is important to understand the mechanisms involved in nutrient absorption in chicken. In the gastrointestinal tract (GIT), the microbiota plays a central role in enhancing nutrient absorption and strengthening the immune system, thereby affecting both growth and health of chicken. There is little information on the diversity and functions of chicken GIT microbiota, its impact on the host, and the interactions between the microbiota and host. Here, we review the recent metagenomic strategies to analyze the chicken GIT microbiota composition and its functions related to improving metabolism and health. We summarize methodology of metagenomics in order to obtain bacterial taxonomy and functional inferences of the GIT microbiota and suggest a set of indicator genes for monitoring and manipulating the microbiota to promote host health in future.

The Himalaya with its altitude and geographical position forms a barrier to atmospheric transport, which produces much aqueous-particle monsoon precipitation and makes it the largest continuous ice-covered area outside polar regions. There is a paucity of data on high-altitude microbial communities, their native environments and responses to environmental-spatial variables relative to seasonal and deglaciation events.Soils were sampled along altitude transects from 5000 m to 6000 m to determine environmental, spatial and seasonal factors structuring bacterial communities characterized by 16 S rRNA gene deep sequencing. Dust traps and fresh-snow samples were used to assess dust abundance and viability, community structure and abundance of dust associated microbial communities. Significantly different habitats among the altitude-transect samples corresponded to both phylogenetically distant and closely-related communities at distances as short as 50 m showing high community spatial divergence. High within-group variability that was related to an order of magnitude higher dust deposition obscured seasonal and temporal rearrangements in microbial communities. Although dust particle and associated cell deposition rates were highly correlated, seasonal dust communities of bacteria were distinct and differed significantly from recipient soil communities. Analysis of closest relatives to dust OTUs, HYSPLIT back-calculation of airmass trajectories and small dust particle size (4-12 µm) suggested that the deposited dust and microbes came from distant continental, lacustrine and marine sources, e.g. Sahara, India, Caspian Sea and Tibetan plateau. Cyanobacteria represented less than 0.5% of microbial communities suggesting that the microbial communities benefitted from (co)deposited carbon which was reflected in the psychrotolerant nature of dust-particle associated bacteria.The spatial, environmental and temporal complexity of the high-altitude soils of the Himalaya generates ongoing disturbance and colonization events that subject heterogeneous microniches to stochastic colonization by far away dust associated microbes and result in the observed spatially divergent bacterial communities.