Region Of Ribosomal RNA Research Articles

Molecular epidemiology and subtyping of Blastocystis sp. and its subtypes in celiac patients; a case control study

Blastocystis sp. is a common intestinal protist, reported from symptomatic and asymptomatic subjects. Blastocystis sp. has been reported from a broad spectrum of gastrointestinal disorders. Celiac disease (CD) is an autoimmune disorder of the small intestine, which leads to the lack of tolerance against gluten. Long-term following of gluten-free diet in CD patients decreases the gut microbiota restoration and probably decreases the chance of Blastocystis sp. colonization. The current study aimed to investigate the prevalence of Blastocystis sp. and its subtypes in CD patients in comparison to healthy subjects. Stool samples were collected from 238 participants including 92 confirmed CD patients and 146 healthy subjects. Upon DNA extraction, the presence of Blastocystis sp. was evaluated using amplification of discriminative regions of the small ribosomal RNA (ssu rRNA) gene. To characterize subtypes and alleles, amplified fragments were sequenced. Phylogenetic trees were constructed to visualize subtype correlation. Our findings showed that 21% (50) of samples including 16.3% (15/92) and 23.97% (35/146) were positive for Blastocystis sp. in CD patients and healthy controls, respectively. Except family relationship, other variables were not statistical correlated with the presence of Blastocystis sp.. Totally, 25 samples were successfully sequenced. Accordingly, ST1, ST2, and ST3 were characterized in 8 (32%), 9 (36%), and 8 (32%) of samples, respectively. Allele discrimination showed that all ST1 were allele 4; alleles 11, 9, and 12 were retrieved from ST2, and alleles 34, 36, and 38 were observed in ST3. The relationship between colonization of Blastocystis sp. and alteration in the gut microbiota composition is indeterminate, however, this hypothesis that following gluten-free diet in CD patients may affect the colonization of Blastocystis sp. via alteration in the gut microbiota composition could be interesting for further investigations.

First Report of Leaf Spot Disease Caused by Boeremia linicola on Trifolium repens in China.

Trifolium repens L. (White clover) a multipurpose legume crop, primarily utilized as a green manure in China. In March 2018, field investigations showed that a leaf spot disease occurred on T. repens in three fields with 50% to 80% incidence (50 plants in each field were investigated) in Nanchong City, Sichuan Province of China. Infected leaves showed symptoms of irregular dark brown spots in the center of leaves or at the leaf margins. Symptomatic leaves were surface sterilized with 3% NaClO for 3 min followed by 75% ethanol for 30 s and then rinsed in sterile water three times. Thereafter, tissue samples from margins of individual lesions were placed on potato dextrose agar and incubated at 25°C in the dark. Four pure cultures (Y3-1; Y3-2; Y3-3; Y3-4) were obtained by single spore isolation. On oatmeal agar medium, a colony reached 57 mm diameter after 9 d in alternating light and dark at 25℃. Fimbriate aerial hypha were flat and compact with pale brown to dark brown color. Conidiogenous cells were hyaline, smooth, ampulliform to doliiform (n = 30), ranging from 4.1 to 10.5 μm long (6.6 ± 1.8 µm) × 2.2 to 5.7 μm wide (4.1 ± 0.8 µm). Conidia were ellipsoidal to cylindrical, hyaline, thin walled, smooth, aseptate, with 2 to 4 polar guttules (n = 50), ranging from 3.2 to 11.3 μm long (6.3 ± 1.1 µm) × 2.1 to 4.1 μm wide (2.8 ± 0.4 µm). Conidial matrix was whitish. Morphologically these isolates resembled species in Boeremia (Chen et al. 2015). Genomic DNA of each culture was extracted from mycelia using the quick and safe method (Chi et al. 2009). The 28S large subunit of nuclear ribosomal RNA (LSU) region, internal transcribed spacer (ITS) region, RNA polymerase II second largest subunit (RPB2), translation elongation factor 1-α (TEF 1-α), β-Tubulin (TUB2) were amplified with corresponding primers (Carbone and Kohn 1999; Liu et al. 1999; Rehner and Samuels 1994; Sung et al. 2007; Vilgalys and Hester 1990; White et al. 1990; Woudenberg et al.2009). Sequences were deposited in GenBank with accession numbers: ON705759 to ON705766, ON734043 to ON734046 and ON841585 to ON841592. Phylogenetic analysis was conducted with combined sequences of the five loci using the maximum likelihood (ML) and the maximum parsimony (MP) methods. The four isolates and the extype strain of B. linicola (CBS 116.76) clustered together with high bootstrap support (BS) values (MLBS = 100; MPBS = 98). All sequences showed 100% identity to those of CBS 116.76, except the ITS region of our isolates (ON705759 to ON705762), which show 99.6% identity to that of CBS 116.76. Based on morphological characteristics and phylogenetic results, our isolates were identified as B. linicola, although the morphological characteristics of CBS 116.76 had not been characterized. To assess pathogenicity, a conidial suspension (approximately 105 CFU/mL) of isolate Y3-1 was sprayed on 1-month-old healthy plants in a greenhouse at 22℃ to 28℃. Plants sprayed with sterilized water were used as negative controls. The test was conducted three times, each with 3 plants. After 10 days, the leaves of the plants showed irregular brown lesions that were similar to the symptoms observed in the field, control plants remained healthy. The pathogen was reisolated and confirmed to be B. linicola, thus completing the verification of Koch's Postulates. Compared to B. exigua, a causal pathogen associated with leaf spot on white clover reported by Wang et al (Wang et al. 2021), B. linicola produced larger conidia, and the two species did not cluster together in the phylogenetic tree. To our knowledge, this is the first report of leaf spot disease caused by B. linicola on Trifolium repens in China.

The composition and function profile of the gut microbiota of patients with primary Sjögren's syndrome.

This healthy volunteer control-based study was conducted to explore alterations of compositions and function of gut microbiota in Chinese pSS patients. The high-throughput Illumina Miseq sequencing method, targeting the V3-V4 region of the 16S ribosomal RNA (rRNA) gene, was used to compare the microbiota communities between 30 pSS patients and 30 age-matched healthy volunteers. The intestinal dysbiosis of pSS patients was evaluated and its correlation with some disease phenotypes was analyzed. Furthermore, we performed the amino acid sequence alignment analysis to illustrate the molecular mimicry patterns of new microbial peptides. Compared with that in healthy controls, the composition and function of the gut microbiota significantly differed in pSS patients. Certain genera and species, including genera: Escherichia-Shigella, Sardovia, Veillonella, Insteinimonas, and Lactobacillales; species: Escherichia coli, Lactobacillus phage Sal3, Lactobacillus reuteri, Lactobacillus gasseri, Streptococcus lutetiensis, Streptococcus mutans, Scardovia wiggsiae, and Fusobacterrium ulcerans were found to be enriched in the feces of pSS patients, while butyrate-producing bacteria were less abundant in pSS patients. Certain genera (including Lactobacillales) and species (including Lactobacillus gasseri) were associated with disease severity and therapy resistance parameters. Autoantigen epitopes of "WPSALPT, NPARSFG, MNPARSFG, and AFGLAIGT" from aquaporin-5 were aligned perfectly with one enriched microbiota of patients with pSS, namely Escherichia coli. The composition and function of the gut microbiota significantly differed in pSS patients compared with that in healthy controls. Our study would facilitate the possible research on the role of gut microbiota in the pathogenesis of pSS.

The oral microbiome of implant-abutment screw holes compared with the peri-implant sulcus and natural supragingival plaque in healthy individuals.

An implant-supported prosthesis consists of an implant fixture, an abutment, an internal screw that connects the abutment to the implant fixture, and the upper prosthesis. Numerous studies have investigated the microorganisms present on the implant surface, surrounding tissues, and the subgingival microflora associated with peri-implantitis. However, there is limited information regarding the microbiome within the internal screw space. In this study, microbial samples were collected from the supragingival surfaces of natural teeth, the peri-implant sulcus, and the implant-abutment screw hole, in order to characterize the microbiome of the internal screw space in healthy subjects. Samples were obtained from the supragingival region of natural teeth, the peri-implant sulcus, and the implant screw hole in 20 healthy subjects. DNA was extracted, and the V3-V4 region of the 16S ribosomal RNA was sequenced for microbiome analysis. Alpha diversity, beta diversity, linear discriminant analysis effect size (LEfSe), and network analysis were employed to compare the characteristics of the microbiomes. We observed significant differences in beta diversity among the samples. Upon analyzing the significant taxa using LEfSe, the microbial composition of the implant-abutment screw hole's microbiome was found to be similar to that of the other sampling sites' microbiomes. Moreover, the microbiome network analysis revealed a unique network complexity in samples obtained from the implant screw hole compared to those from the other sampling sites. The bacterial composition of the biofilm collected from the implant-abutment screw hole exhibited significant differences compared to the supra-structure of the implant. Therefore, long-term monitoring and management of not only the peri-implant tissue but also the implant screw are necessary.

Prevalence and Subtype Distribution of Blastocystis Isolated from School-Aged Children in the Thai-Myanmar Border, Ratchaburi Province, Thailand

Blastocystis is one of the most common enteric protozoa that inhabits the intestinal tract of humans and different animals. Moreover, it has a worldwide geographic distribution. Its main mode of transmission is via the fecal-oral route. At present, 26 subtypes are widely distributed across both humans and animals. The current study aimed to determine the prevalence and subtype distribution of Blastocystis among school-aged children living on the Thai-Myanmar border, Ratchaburi province, Thailand. In total, 508 samples were collected from children at six schools. The prevalence of Blastocystis infection was amplified and sequenced in the 600 bp barcode region of the small-subunit ribosomal RNA (SSU rRNA). The overall prevalence of Blastocystis infection was 3.35% (17/508). ST3 (11/17) was the most predominant subtype, followed by ST1 (5/17) and ST2 (1/17). A phylogenetic tree was constructed based on the Tamura92+G+I model using the maximum-likelihood algorithm. Surprisingly, all sequences of the ST3-positive samples were closely correlated with the cattle-derived sequence. Meanwhile, all sequences of the Blastocystis ST1-positive samples were closely correlated with the human-derived sequence. Nevertheless, further studies should be conducted to validate the zoonotic transmission of Blastocystis. Based on our findings, personal hygiene and sanitation should be improved to promote better health in children in this area.

Discovery of a New Genus and Species of Allocreadiidae (Trematoda) in Mexico: Mesoamericatrema Magnisacculus n. Gen. n. Sp.

The trematodes of Allocreadiidae are mainly parasites of freshwater fish and the family contains 18 valid genera. Since 2004, 4 genera have been described in the Americas: Paracreptotrema, Paracreptotrematoides, Pseudoparacreptotrema and Auriculostoma, of which the latter was recently synonymized with Creptotrema by Franceschini et al., (2021). During a study in 2018 on fish parasites of Lacantún River, Chiapas, Mexico, allocreadiids were collected from the intestine of Atherinella alvarezi and morphological differences with other genera of the family were immediately noted. These differences were corroborated with molecular data and phylogenetic analyses, which indicated that it was a new genus and species. The objective of this study is to describe the new taxon, which we name Mesoamericatrema magnisacculus n. gen., n. sp. as well as to clarify its phylogenetic relationships, host specificity, and geographical distribution. For this, we carried out a meticulous study of the morphology and compared the new taxon with its congeners. We also obtained sequences of the 28S and ITS from the ribosomal RNA region that were used in generating molecular phylogenies and in calculating genetic distances with sequences of other species of Allocreadiidae available in the Genbank. The new genus is mainly characterized by having a very large cirrus sac in relation to the length of its body and nests in a clade that groups Creptotrema, Creptotrematina, Paracreptotrema, Paracreptotrematoides, Pseudoparacreptotrema and Wallinia, all of which have a Neotropical affinity in terms of their geographic and host distribution. Mesoamericatrema n. gen. is the fifth genus of Allocreadiidae to be described in the Americas since 2004, the third discovered in Mexico since 2016, and the first to be described as parasitizing Atheriniformes, which indicates that Middle America is a region where important speciation events have occurred in freshwater fish parasites.

Estimation of the post-mortem interval by modelling the changes in oral bacterial diversity during decomposition.

Decomposition, a complicated process, depends on several factors, including carrion insects, bacteria and the environment. However, the composition of and variation in oral bacteria over long periods of decomposition remain unclear. The current study aims to illustrate the composition of oral bacteria and construct an informative model for estimating the post-mortem interval (PMI) during decomposition. Samples were collected from rats' oral cavities for 59 days, and 12 time points in the PMI were selected to detect bacterial community structure by sequencing the V3-V4 region of the bacterial 16S ribosomal RNA (16S rRNA) gene on the Ion S5 XL platform. The results indicated that microorganisms in the oral cavity underwent great changes during decomposition, with a tendency for variation to first decrease and then increase at day 24. Additionally, to predict the PMI, an informative model was established using the random forest algorithm. Three genera of bacteria (Atopostipes, Facklamia and Cerasibacillus) were linearly correlated at all 12 time points in the 59-day period. Planococcaceae was selected as the best feature for the last 6 time points. The R2 of the model reached 93.94%, which suggested high predictive accuracy. Furthermore, to predict the functions of the oral microbiota, PICRUSt results showed that energy metabolism was increased on day 3 post-mortem and carbohydrate metabolism surged significantly on days 3 and 24 post-mortem. Overall, our results suggested that post-mortem oral microbial community data can serve as a forensic resource to estimate the PMI over long time periods. The results of the present study are beneficial for estimating the PMI. Identifying changes in the bacterial community is of great significance for further understanding the applicability of oral flora in forensic medicine.

A new species of Cleruchus (Hymenoptera, Mymaridae), an egg parasitoid of the invasive Cis chinensis (Coleoptera, Ciidae) in Switzerland, with new records of other congeners in Europe

A fairyfly (Hymenoptera, Mymaridae) Cleruchus breviclava Triapitsyn & Coray, sp. nov. is described and illustrated. The new species is an egg parasitoid of the invasive Cis chinensis Lawrence (Coleoptera, Ciidae) in Antrodia xantha fungus (Polyporales, Fomitopsidaceae) in Basel, Switzerland; it is also known from low mountains in Germany and Switzerland. Supporting data on the “barcoding” region of the mitochondrial cytochrome c oxidase subunit I gene, as well as separate regions of nuclear ribosomal RNA, the D2 region of 28S and the internal transcribed spacer 2, provide strong evidence of conspecificity of the morphologically variable macropterous and strongly brachypterous individuals of C. breviclava. Macropterous females of the new species are most similar to those of C. detritus Bakkendorf, also known from Switzerland. New records are provided for some other species of Cleruchus Enock in Europe. A key to both sexes of the described European species of the genus is given.

Exploring the alterations and function of skin microbiome mediated by ionizing radiation injury.

Radiation-induced skin injury (RISI) is still the most common and severe side effect of radiotherapy. The role of the skin's microbial barrier in the pathogenesis and progression of RISI needs to be fully investigated. This study aimed to explore the alterations in and functions of the skin microbiota in RISI. We applied the unculturable approach to characterize the cutaneous microbiomes of a radiation-induced animal model by sequencing the V1-V3 regions of the 16S ribosomal RNA (rRNA) gene. Combined with the downloaded clinical data of patients, a comprehensive analysis was performed to identify potential radioprotective species and metabolic pathways. There were no significant differences in the alpha diversity indices (Sobs, Shannon, Simpson, Ace, and Chao) between the acute radiation injury and control groups. Phylum-level analysis of the RISI microbiomes exhibited significant predominance of Firmicutes (mean abundance=67%, corrected p=0.0035). The high abundance of Firmicutes was significantly associated with rapid healing of RISI (average relative abundance=52%; Kruskal-Wallis: p=5.7E-4). Among its members, Streptococcus, Staphylococcus, Acetivibrio ethanolgignens group, Peptostreptococcus, Anaerofilum, and UCG-002 [linear discriminant analysis (LDA)>3, p<0.05] were identified as the core genera of Firmicutes. In addition, Lachnosiraceae and Lactobacillus occupied an important position in the interaction network (r>0.6, p<0.05). The differential metabolic pathways of RISI were mainly associated with carbohydrate metabolism (butanoate and propanoate metabolism), amino acid metabolism (tryptophan and histidine metabolism), energy metabolism, and lipid metabolism (fatty acid degradation and biosynthesis). This study provides new insights into the potential mechanism and skin microbial changes in the progression of RISI. The overwhelming predominance of members of Firmicutes, including Streptococcaceae, Staphylococcaceae, Lachnospiraceae, and Lactobacillus, is potentially related to rapid healing of RISI. The microbiota-metabolite axis plays a critical role in RISI and provides promising therapeutic targets for the treatment of adverse side effects.

Comparison of iSeq and MiSeq as the two platforms for 16S rRNA sequencing in the study of the gut of rat microbiome

Amplicon-based next-generation sequencing (NGS) of the 16S ribosomal RNA (16S) regions is a culture-free method used to identify and analyze Procaryota occurring within a given sample. The prokaryotic 16S rRNA gene contains conserved regions and nine variable regions (V1-V9) frequently used for phylogenetic classification of genus or species in diverse microbial populations. This work compares the accuracy and efficacy of two platforms, iSeq and MiSeq from Illumina, used in sequencing 16S rRNA. The most important similarities and differences of 16S microbiome sequencing in 20 fecal rat samples were described. Genetic libraries were prepared according to 16S Metagenomic Sequencing Library Preparation (Illumina) for the V3 and V4 regions of the 16S. The species richness obtained using iSeq technology was lower compared to MiSeq. At the second taxonomy level (L2), the abundance of taxa was comparable for both platforms. At the L7, the taxa abundance was significantly different, and the number of taxa was higher for the MiSeq. The alpha diversity was lower for iSeq than for MiSeq, starting from the order to the species level. The beta diversity estimation revealed statistically significant differences in microbiota diversity starting from the class level to the species level in samples sequenced on two investigated platforms. This work disclosed that the iSeq platform could be used to evaluate the bacterial profile of the samples to characterize the overall profile. The MiSeq System seems to be better for a detailed analysis of the differences in the microbiota composition.Key points• iSeq platform allows to shorten the sequencing time three times compared to the MiSeq.• iSeq can only be used for an initial and quick microbiome assessment.• MiSeq is better for a detailed analysis of the differences in the microbiota composition.

ТАКСОНОМИЧЕСКАЯ ХАРАКТЕРИСТИКА МИКРОБИОТЫ ТОЛСТОГО КИШЕЧНИКА И ЕЕ ВЗАИМОСВЯЗЬ С ЭНДОКРИННОЙ СИСТЕМОЙ У ДЕТЕЙ И ПОДРОСТКОВ С ИЗБЫТОЧНОЙ МАССОЙ ТЕЛА И ОЖИРЕНИЕМ

Composition of the intestinal microbiota and its influence on human metabolism, including hormone synthesis, has been studied in many research works, but the data obtained as yet does not allow forming the general idea of microbiota composition in overweight and obese individuals. The purpose of the research was to determine the internal microbiota composition and its relationship with certain hormones in children against the background of weight gain. A single-stage single-center comparative study was carried out in parallel groups in Dec. 2018 - May 2021, which included 74 children, of which 38 (51.3%) boys and 36 (48.6%) girls, median age 12.1 [10.8; 14.6] years old, with overweight and constitutional-exogenous obesity (CEO) of different grades compared to 44 healthy children (26 (59.09%) boys and 18 (40.9%) girls, median age 13.1 [10.5; 13.8] years old). The anthropometric assessment included: measuring height with 1-millimeter accuracy; body weight with 100-gram accuracy (without shoes and outerwear on the scales). The calculation of BMI SDS and height SDS was carried out using the software developed by the WHO, “AnthroPlus,” for children aged 6 to 19 years old with the BMI SDS formula used as follows: (x-X)/SD, where x is the patient's BMI, X is the average BMI for a given age and gender, SD is the standard deviation of the BMI index for a given age and gender. The investigation of the intestinal microbiota using the DNA metagenomic sequencing of stool samples (sequencing the V4 region of 16S ribosomal RNA (rRNA) gene) was carried out using the QIAamp® PowerFecal® DNA Kit by QIAGEN in accordance with the manufacturer's instructions at the laboratory facilities of the “Knomics” microbiome research company (Skolkovo, Moscow, Russia). The levels of leptin, insulin, irisin, resistin, GLP-1 and GLP-2 were evaluated in blood serum by ELISA using the laboratory kits from the CLOUD-CLONE CORP. (CCC, USA) using the enzyme immunoassay reactions analyzer UNIPLAN (Russia). The information about the following taxonomic composition of the intestinal microbiota was obtained during the research: the level of Firmicutes demonstrated the absence of a statistically significant difference in the groups (p=0.645); the level of Actinobacteriota and Euryarchaeota was statistically significantly higher in group 1 (in overweight and obese children and adolescents) than in group 2 (p=0.002 and p=0.002, respectively); the level of Bacteroidota was statistically significantly lower in group 1 than in group 2 (p&lt; 0.001); statistically significantly lower level of certain hormones in group 1 compared to group 2 (glucagon (p=0.001), resistin (p=0.019), GLP-1 (p&lt;0.001), and GLP-2 (p&lt; 0.001)); statistically significantly higher concentration of insulin (p=0.001) and leptin (p=0.008). Statistically significantly higher levels of the following bacterial genus were revealed in microbiota in children from group 1 compared to the control group 2: Bifidobacterium (p=0.007); Agathobacter (p=0.002); Dorea (p=0.001); Blautia (p=0.016); Lachnoclostridium (p=0.012); Roseburia (p=0.012); Collinsella (p&lt;0.001); and Holdemanella (p=0.034), while statistically significantly lower levels of: Faecalibacterium (p&lt;0.001); Subdoligranulum (p&lt;0.001); Bacteroides_vulgatus (p=0.042); Bacteroides (p=0.001); Bacteroidesmassiliensis (p=0.002); Bacteroides_eggerthii, Alistipes (p&lt;0.001); and Parabacteroides_merdae (p=0.002). The data on the average multidirectional and insignificant correlations of microbiota composition and hormone levels in obese children compared to the children and adolescents from healthy group have been obtained as well, which requires further studying. The decrease in the strength of the relationship between specific representatives of the intestinal microbiota and the level of certain hormones in overweight and obese children obtained in this research is probably associated with an imbalance in the “microbiota-metabolism” axis.

Gut microbiota composition reflects disease progression, severity and outcome, and dysfunctional immune responses in patients with hypertensive intracerebral hemorrhage.

In this study, we aimed to explore the alterations in gut microbiota composition and cytokine responses related to disease progression, severity, and outcomes in patients with hypertensive intracerebral hemorrhage (ICH). Fecal microbiota communities of 64 patients with ICH, 46 coronary heart disease controls, and 23 healthy controls were measured by sequencing the V3-V4 region of the 16S ribosomal RNA (16S rRNA) gene. Serum concentrations of a broad spectrum of cytokines were examined by liquid chips and ELISA. Relationships between clinical phenotypes, microbiotas, and cytokine responses were analyzed in the group with ICH and stroke-associated pneumonia (SAP), the major complication of ICH. In comparison with the control groups, the gut microbiota of the patients with ICH had increased microbial richness and diversity, an expanded spectrum of facultative anaerobes and opportunistic pathogens, and depletion of anaerobes. Enterococcus enrichment and Prevotella depletion were more significant in the ICH group and were associated with the severity and functional outcome of ICH. Furthermore, Enterococcus enrichment and Prevotella depletion were also noted in the SAP group in contrast to the non-SAP group. Enterococci were also promising factors in the prognosis of ICH. The onset of ICH induced massive, rapid activation of the peripheral immune system. There were 12 cytokines (Eotaxin, GM-CSF, IL-8, IL-9, IL-10, IL-12p70, IL-15, IL-23, IL-1RA, IP-10, RANTES, and TNF-α) changed significantly with prolongation of ICH, and the Th2 responses correlated with the 90-day outcomes. Cytokines TNF-α, IP-10, IL-1RA, IL-8, IL-18, and MIP-1β in SAP group significantly differed from non-SAP group. Among these cytokines, only IP-10 levels decreased in the SAP group. Enterococcus was positively associated with IL-1RA and negatively associated with IP-10, while Prevotella was inversely associated in both the ICH and SAP groups. This study revealed that gut dysbiosis with enriched Enterococcus and depleted Prevotella increased the risk of ICH and subsequently SAP. The altered gut microbiota composition and serum cytokine profiles are potential biomarkers that reflect the inciting physiologic insult/stress involved with ICH.

Season, Vegetation Proximity and Building Age Shape the Indoor Fungal Communities' Composition at City-Scale.

Exposure to particular microbiome compositions in the built environment can affect human health and well-being. Identifying the drivers of these indoor microbial assemblages is key to controlling the microbiota of the built environment. In the present study, we used culture and metabarcoding of the fungal Internal Transcribed Spacer ribosomal RNA region to assess whether small-scale variation in the built environment influences the diversity, composition and structure of indoor air fungal communities between a heating and an unheated season. Passive dust collectors were used to collect airborne fungi from 259 dwellings representative of three major building periods and five building environments in one city—Lausanne (Vaud, Switzerland)—over a heating and an unheated period. A homogenous population (one or two people with an average age of 75 years) inhabited the households. Geographic information systems were used to assess detailed site characteristics (altitude, proximity to forest, fields and parks, proximity to the lake, and density of buildings and roads) for each building. Our analysis indicated that season was the factor that explained most of the variation in colonies forming unit (CFU) concentration and indoor mycobiome composition, followed by the period of building construction. Fungal assemblages were more diverse during the heating season than during the unheated season. Buildings with effective insulation had distinct mycobiome compositions from those built before 1975 — regardless of whether they were constructed with pre-1945 technology and materials or 1945 — 1974 ones. The urban landscape—as a whole—was a significant predictor of cultivable Penicillium load—the closer the building was to the lake, the higher the Penicillium load—but not of fungal community composition. Nevertheless, the relative abundance of eleven fungal taxa detected by metabarcoding decreased significantly with the urbanization gradient. When urban landscape descriptors were analyzed separately, the explanatory power of proximity to vegetation in shaping fungal assemblages become significant, indicating that land cover type had an influence on fungal community structure that was obscured by the effects of building age and sampling season. In conclusion, indoor mycobiomes are strongly modulated by season, and their assemblages are shaped by the effectiveness of building insulation, but are weakly influenced by the urban landscape.

LUNG AND GUT MICROBIOME DURING EARLY-LIFE RESPIRATORY SYNCYTIAL VIRUS INFECTION

LUNG AND GUT MICROBIOME DURING EARLY-LIFE RESPIRATORY SYNCYTIAL VIRUS INFECTION

Assessing the effect of antihypertensives on plaque microbiota in patients with periodontitis and hypertension using 16S rRNA sequencing: A cross-sectional study.

Periodontitis is initiated or accelerated by dysbiosis of oral microorganisms. When hypertension is accompanied in periodontitis patients, changes of oral microbiota occur. Since there are no reports on antihypertensives, we assessed their effect on the oral microbial profiles of patients with periodontitis. This study involved 95 participants divided into two groups: those with periodontitis and hypertension (P_HT), and those with periodontitis and taking medications for hypertension (P_mHT). Plaque samples were collected from the buccal, supragingival, and subgingival sites of the oral cavities of these patients. DNA was extracted, and the V3-V4 region of the 16S ribosomal RNA was sequenced and analyzed. The P_HT and P_mHT groups were similar with respect to the alpha- and beta-diversity as well as the dominant phyla and genera, but differed in the relative abundance of bacterial species (85 species). In the P_mHT group, the relative abundance of major periodontal pathogens was greatly increased. In particular, Tannerella forsythia, Treponema denticola, and Fretibacterium fastidiosum increased nearly three times in the linear discriminant analysis score in the supragingival plaque. Also, there was an increase in the relative abundance of Prevotella spp., associated with periodontitis and nitrate reduction, which was also evident in the supragingival plaque. These findings indicate that antihypertensives induce dysbiotic changes in the oral microbiota of patients with periodontitis, which are associated with increases in the relative abundance of periodontal pathogens. Therefore, more active periodontal treatment and supportive periodontal therapy are required in patients taking antihypertensives.

Mycena subpiligera sp. nov., a Symbiotic Species from China Associated with the Seed Germination of Gastrodia elata

Mycena subpiligera, a new taxon in sect. Fragilipedes that can strongly enhance the germination efficiency of Gastrodia elata seeds, was discovered in subtropical areas of China. As revealed by a morphological comparison with related Mycena species as well as maximum likelihood (ML) and Bayesian phylogenetic analyses based on sequences of the internal transcribed spacer (ITS) and the large subunit (LSU) regions of nuclear ribosomal RNA, the new taxon can be distinguished from phenotypically similar and phylogenetically related species. Optimal cultural conditions for M. subpiligera basidiomata are reported, and the germination rate of the new species is compared with that of M. citrinomarginata.

Epidermal Barrier Integrity is Associated with Both Skin Microbiome Diversity and Composition in Patients with Acne Vulgaris.

BackgroundAlthough the changed lipid environment of the pilosebaceous unit and the growth of lipophilic Cutibacterium acnes (C. acnes) during puberty has long been considered as the trigger of acne vulgaris, the involvement of the interaction between the epidermal barrier integrity and the skin microbiome in this disease has not been fully elucidated.ObjectiveThe aim of this study was to analyze the differences in the epidermal barrier and skin microbiota in patients with acne vulgaris and their correlation.MethodsThe skin microbial samples and epidermal barrier data from 74 acne patients and 19 healthy subjects were collected in this cross-sectional study. The microbial diversity was analyzed based on a high-throughput sequencing approach that targets the V3-V4 region of the bacteria 16S ribosomal RNA genes.ResultsCompared with healthy controls, acne patients had significantly increased transepidermal water loss (TEWL), pH levels, sebum, porphyrins, and red areas, and reduced skin microbiome diversity according to the goods coverage diversity index (p = 0.021), Shannon diversity index (p = 0.037), and Simpson diversity index (p = 0.023). Moreover, the diversity gradually decreased with the increase in acne grading. Based on the principal coordinate analysis (PCoA) analysis plot, the skin microbiota of acne patients and healthy controls could be divided into two different sets, which could not be used to separate acne patients with different disease severity. Finally, this study found that both TEWL and sebum were negatively associated with the Shannon and Simpson diversity index. Meanwhile, the taxa Enhydrobacter and Stenotrophomonas were positively associated with TEWL, stratum corneum hydration, respectively.ConclusionThis study demonstrated that acne vulgaris exists in patients with both damaged epithelial barriers and associated microbiota dysbiosis; the findings will help improve the understanding of the disease and may contribute to the development of better treatment options.

Detection of A2143G, A2142C, and A2142G Point Mutations with Real-Time PCR in Stool Specimens from Children Infected with Helicobacter pylori.

Reports have indicated an increasing prevalence of clarithromycin resistance in children relative to adults. Thus, it is important to investigate primary clarithromycin resistance before therapy to avoid treatment failure. A2142G, A2143G, and A2142C point mutations in the peptidyltransferase region of the 23S ribosomal RNA (rRNA) of Helicobacter pylori (H. pylori) strains isolated from children with gastrointestinal symptoms and asymptomatic children were evaluated via real-time polymerase chain reaction (RT-PCR) using fecal DNA samples. The presence of H. pylori was determined using a fecal H. pylori antigen enzyme-linked immunosorbent assay (ELISA) kit from the stools of children (n = 543). A2143G, A2142C, and A2142G point mutations were detected via RT-PCR and confirmed by sequencing the 23S rDNA. Fecal H. pylori antigen testing was positive in 101 symptomatic (49) and asymptomatic (52) children. A significant difference was found between the 0–5- and 5–18-year-old groups in terms of the A2143G and A2142G point mutations (p = 0.001). The A2142C mutation was not detected. There was a significant difference in the A2143G mutation between the symptomatic and asymptomatic 5–18-year-old children (p = 0.019). Macrolides are frequently used to treat upper respiratory tract infections in children due to their selective pressure effect. We suggest that H. pylori strains carrying mutations in the 23S RNA subunit conferring clarithromycin resistance may lead to an intense inflammatory response in the gastric epithelial cells, allowing them to proliferate more rapidly and causing possible diarrhea, halitosis, or abdominal pain in children.

Identification and a culture method for a Helicotylenchus microlobus from tomato in China

BackgroundThe nematodes of the genus Helicotylenchus are root parasites of a wide variety of plants, and certain species can cause serious damage to their hosts. During a survey of the plant-parasitic nematode associated with tomato, a population of Helicotylenchus was collected from tomato roots and soil samples. Thus, one of the objectives of the study was to confirm the specie of Helicotylenchus obtained from the tomato samples based on morphological and molecular characteristics. In addition, a mass pure culture of plant-parasitic nematodes is key to pathogenicity studies and many other biological studies. However, a successful mass rearing method for Helicotylenchus has not been reported. Thus, the other objective of the study was to establish a method of culturing Helicotylenchus.ResultsBased on both the morphological characteristics and molecular analysis of the internal transcribed spacer (ITS) and D2-D3 expansion region of 28S ribosomal RNA (rRNA) sequences the specimens were identified as Helicotylenchus microlobus. Phylogenetic analysis with the rRNA sequences of the ITS and 28S D2-D3 regions was consistent with molecular identification, suggesting this population formed a highly supported clade with other H. microlobus populations. Additionally, a method for culture of H. microlobus on carrot disks was established, and the effect of temperature on the reproduction rate (Rr) of H. microlobus was investigated. The optimum temperature for culturing H. microlobus on carrot disks was 27.5 °C and, after inoculation with 30 females of H. microlobus at 27.5 °C for 90 days, Rr reached 406.ConclusionsTo our knowledge, this is the first detailed description of H. microlobus from tomato in China. This study also demonstrated that the carrot disk method is suitable for the culture of H. microlobus. This study lays a foundation for other related research on H. microlobus, and has significance for the study of Helicotylenchus.

MicrobiomeGWAS: A Tool for Identifying Host Genetic Variants Associated with Microbiome Composition

The microbiome is the collection of all microbial genes and can be investigated by sequencing highly variable regions of 16S ribosomal RNA (rRNA) genes. Evidence suggests that environmental factors and host genetics may interact to impact human microbiome composition. Identifying host genetic variants associated with human microbiome composition not only provides clues for characterizing microbiome variation but also helps to elucidate biological mechanisms of genetic associations, prioritize genetic variants, and improve genetic risk prediction. Since a microbiota functions as a community, it is best characterized by β diversity; that is, a pairwise distance matrix. We develop a statistical framework and a computationally efficient software package, microbiomeGWAS, for identifying host genetic variants associated with microbiome β diversity with or without interacting with an environmental factor. We show that the score statistics have positive skewness and kurtosis due to the dependent nature of the pairwise data, which makes p-value approximations based on asymptotic distributions unacceptably liberal. By correcting for skewness and kurtosis, we develop accurate p-value approximations, whose accuracy was verified by extensive simulations. We exemplify our methods by analyzing a set of 147 genotyped subjects with 16S rRNA microbiome profiles from non-malignant lung tissues. Correcting for skewness and kurtosis eliminated the dramatic deviation in the quantile–quantile plots. We provided preliminary evidence that six established lung cancer risk SNPs were collectively associated with microbiome composition for both unweighted (p = 0.0032) and weighted (p = 0.011) UniFrac distance matrices. In summary, our methods will facilitate analyzing large-scale genome-wide association studies of the human microbiome.