Phylum-level Analysis Research Articles

Consumption of poly-γ-glutamate-vitamin B6 supplement and urinary microbiota profiles in Korean healthy adults: a randomized, double-blinded, placebo-controlled intervention study.

Poly-γ-glutamic acid (γ-PGA), a natural polymer found in fermented soybean products, has been reported to play a prebiotic role in the gut. This intervention study investigated the effects of γ-PGA-containing supplement consumption on urinary microbiota in healthy adults because of limited data on such investigation. A 4-week parallel trial including 39 male and female Korean adults, who were free of chronic diseases and infection, was designed as a randomized, double-blinded, placebo-controlled study. A total of 30 participants completed the study wherein the intervention group (n = 17) received a mixture supplement containing 600 mg/day of γ-PGA and 100 mg/day of vitamin B6, while the control group (n = 13) received a placebo. Paired datasets (baseline and endpoint data) of microbiota profiles, which were constructed via urinary assays of microbe-derived extracellular vesicles, were analyzed and compared between the two groups. Only the intervention group yielded significant results for the Bray-Curtis and Jaccard dissimilarity indices between baseline and endpoint data (P < 0.05). In the phylum-level analysis of microbial composition, the Firmicutes to Bacteroidetes ratio (FB ratio) tended to decrease from baseline in the intervention group; however, it increased in the control group. Differences between the baseline and endpoint FB ratios were significant between the two groups (P < 0.05). This study's findings suggest that γ-PGA-vitamin B6 supplementation potentially alters the microbial community composition of a host. Further investigation into the biological consequences of commensal microbiota alteration by γ-PGA-containing supplement consumption is warranted.

Duodenal and pancreatic tissue microbiome profiles of PPI users and non-users

Factors that influence the pancreas microbiome are not well understood. Regular proton pump inhibitor (PPI) use induces significant alterations in the gut microbiome, including an increase in the abundance of Streptococcus, and may be associated with pancreatic cancer risk. The aim of this study was to examine whether PPI use is associated with pancreatic and duodenal tissue microbiomes. We compared 16S rRNA microbiome profiles of normal pancreatic and duodenal tissue from 103 patients undergoing pancreatic surgery for non-malignant indications, including 34 patients on PPIs, accounting for factors including age, smoking, body mass index and the presence of main pancreatic duct dilation. Histologically normal tissue from the pancreatic head had higher alpha diversity and enrichment of Firmicutes by phylum-level analysis and Streptococcus species compared to normal pancreas body/tail tissues (16.8 % vs 8.8 %, P = .02, and 5.9 % vs 1.4 %, P = .03, respectively). Measures of beta diversity differed significantly between the pancreas and the duodenum, but in subjects with main pancreatic duct dilation, beta diversity of pancreatic head tissue was more similar to normal duodenal tissue than those without pancreatic duct dilation. Duodenal tissue of PPI users had significant enrichment of Firmicute phyla (34.7 % vs. 14.1 %, P = .01) and Streptococcus genera (19.5 % vs. 5.2 %, P = .01) compared to non-users; these differences were not evident in pancreas tissues. By multivariate analysis, PPI use was associated with alpha diversity in the duodenum, but not in the pancreas. However, some differences in pancreas tissue beta diversity were observed between PPI users and non-users. In summary, we find differences in the microbiome profiles of the pancreas head versus the pancreatic body/tail and we find PPI use is associated with alterations in duodenal and pancreatic tissue microbiome profiles.

Effects of Aeriscardovia aeriphila on growth performance, antioxidant functions, immune responses, and gut microbiota in broiler chickens.

Aeriscardovia aeriphila, also known as Bifidobacterium aerophilum, was first isolated from the caecal contents of pigs and the faeces of cotton-top tamarin. Bifidobacterium species play important roles in preventing intestinal infections, decreasing cholesterol levels, and stimulating the immune system. In this study, we isolated a strain of bacteria from the duodenal contents of broiler chickens, which was identified as A. aeriphila, and then evaluated the effects of A. aeriphila on growth performance, antioxidant functions, immune functions, and gut microbiota in commercial broiler chickens. Chickens were orally gavaged with A. aeriphila (1×109 CFU/mL) for 21 d. The results showed that A. aeriphila treatment significantly increased the average daily gain and reduced the feed conversion ratio (P<0.001). The levels of serum growth hormone (GH) and insulin-like growth factor 1 (IGF-1) were significantly increased following A. aeriphila treatment (P<0.05). Blood urea nitrogen and aspartate aminotransferase levels were decreased, whereas glucose and creatinine levels increased as a result of A. aeriphila treatment. Furthermore, the levels of serum antioxidant enzymes, including catalase (P<0.01), superoxide dismutase (P<0.001), and glutathione peroxidase (P<0.05), and total antioxidant capacity (P<0.05) were enhanced following A. aeriphila treatment. A. aeriphila treatment significantly increased the levels of serum immunoglobulin A (IgA) (P<0.05), IgG (P<0.01), IgM (P<0.05), interleukin-1 (IL-1) (P<0.05), IL-4 (P<0.05), and IL-10 (P<0.05). The broiler chickens in the A. aeriphila group had higher secretory IgA (SIgA) levels in the duodenum (P<0.01), jejunum (P<0.001), and cecum (P<0.001) than those in the control group. The messenger RNA (mRNA) relative expression levels of IL-10 (P<0.05) and IL-4 (P<0.001) in the intestinal mucosa of chickens were increased, while nuclear factor-‍κB (NF‍-‍κB) (P<0.001) expression was decreased in the A. aeriphila group compared to the control group. Phylum-level analysis revealed Firmicutes as the main phylum, followed by Bacteroidetes, in both groups. The data also found that Phascolarctobacterium and Barnesiella were increased in A. aeriphila-treated group. In conclusion, oral administration of A. aeriphila could improve the growth performance, serum antioxidant capacity, immune modulation, and gut health of broilers. Our findings may provide important information for the application of A. aeriphila in poultry production.

Metabolomics Reveals Gut Microbiota Contribute to PPARα Deficiency-Induced Alcoholic Liver Injury.

Incidence and mortality rates of alcoholic liver disease (ALD) is one of the highest in the world. In the present study, we found that the genetic knockout nuclear receptor the peroxisome proliferator-activated receptor α (PPARα) exacerbated ALD. Lipidomics of the liver revealed changed levels of lipid species encompassing phospholipids, ceramides (CM), and long-chain fatty acids in Ppara-null mice induced by ethanol. Moreover, 4-hydroxyphenylacetic acid (4-HPA) was changed as induced by ethanol in the metabolome of urine. Moreover, the phylum level analysis showed a decrease in the level of Bacteroidetes and an increase in the level of Firmicutes after alcohol feeding in Ppara-null mice, while there was no change in wild-type mice. In Ppara-null mice, the level of Clostridium_sensu_stricto_1 and Romboutsia were upregulated after alcohol feeding. These data revealed that PPARα deficiency potentiated alcohol-induced liver injury through promotion of lipid accumulation, changing the metabolome of urine, and increasing the level of Clostridium_sensu_stricto_1 and Romboutsia. 4-HPA could improve ALD in mice by regulating inflammation and lipid metabolism. Therefore, our findings suggest a novel approach to the treatment of ALD: focusing on the gut microbiota and its metabolites. Data are available via ProteomeXchange (PXD 041465).

Effects of Polyphenols and Glucosinolates in Broccoli Extract on Human Gut Microorganisms Based on Simulation In Vitro.

Broccoli extract mainly contains polyphenols and glucosinolates (GSLs). GSLs can be hydrolyzed by gut microorganisms into isothiocyanates (ITCs) and other active substances. These substances have anticancer, anti-inflammatory, antimicrobial, and atherosclerosis-reducing functions. In this study, a high concentration (2000 μmol/L GSLs and 24 μmol/L polyphenols) and a low concentration (83 μmol/L GSLs and 1 μmol/L polyphenols) of broccoli extract were prepared. Gut microorganisms from fresh human feces were cultured to simulate the gut environment in vitro. The GSL content decreased and the types and content of ITCs increased with broccoli extract hydrolysis through cyclic condensation and gas chromatography-mass spectrometry (GC-MS) analyses. Broccoli extract significantly increased probiotics and inhibited harmful bacteria through 16S rDNA sequencing. Based on phylum level analysis, Firmicutes and Lachnospiraceae increased significantly (P < 0.05). At the genus level, both high- and low-concentration groups significantly inhibited Escherichia and increased Bilophila and Alistipes (P < 0.05). The high-concentration group significantly increased Bifidobacterium (P < 0.05). The broccoli extract improved the richness of gut microorganisms and regulated their structure. The GSL hydrolysis was significantly correlated with Bilophila, Lachnospiraceae, Alistipes, Bifidobacterium, Escherichia, and Streptococcus (P < 0.05). These study findings provide a theoretical foundation for further exploring a probiotic mechanism of broccoli extract in the intestine.

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.

Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota

The Terrestrial Miscellaneous Euryarchaeota Group has been identified in various environments, and the single genome investigated thus far suggests that these archaea are anaerobic sulfite reducers. We assemble 35 new genomes from this group that, based on genome analysis, appear to possess aerobic and facultative anaerobic lifestyles and may oxidise rather than reduce sulfite. We propose naming this order (representing 16 genera) “Lutacidiplasmatales” due to their occurrence in various acidic environments and placement within the phylum Thermoplasmatota. Phylum-level analysis reveals that Thermoplasmatota evolution had been punctuated by several periods of high levels of novel gene family acquisition. Several essential metabolisms, such as aerobic respiration and acid tolerance, were likely acquired independently by divergent lineages through convergent evolution rather than inherited from a common ancestor. Ultimately, this study describes the terrestrially prevalent Lutacidiciplasmatales and highlights convergent evolution as an important driving force in the evolution of archaeal lineages.

Comparison of gut microbial communities, free amino acids or fatty acids contents in the muscle of wild Aristichthys nobilis from Xinlicheng reservoir and Chagan lake

BackgroundFish is favored by consumers, while amino acids and fatty acids are the main nutrients of muscle. At present, it has been found that the gut microbial community may be involved in the regulation of host material anabolism. Juvenile and adult bighead carp (A. nobilis) from Chagan lake and Xinlicheng reservoir were selected, and divided into four groups to compare the differences of gut microbial communities, free amino acid and fatty acids in muscle.ResultsThe results showed that fish in different lakes or ages contained specific microbiota, the gut microbial structure was similar, but the microbial content was significantly different. Gut microbial abundance of juvenile fish in Chagan lake was significantly higher than that of other groups. Phylum level analysis Proteobacteria was the dominant gut bacteria of fish in both adult and juvenile fish from two separate lakes. Actinobacteria was another dominant bacterial phylum in juvenile fish in both lakes. Contents of free amino acids and fatty acids in muscle were detected, and the relationships between them and gut microbial communities were analyzed. Bighead carp grew from juvenile to adult, Actinobacteria abundance decreased (P < 0.05) and Proteobacteria increased (P < 0.05). Proteobacteria was positively correlated with the contents of Thr, Lys, Pro, Asp, Gly and Glu, Actinobacteria was negatively correlated with Met and His. Meanwhile, EPA and DHA were positively correlated with Proteobacteria, EPA and DHA were not significantly associated with Actinobacteria.ConclusionIt was speculated that the contents of free amino acids and fatty acids in muscle might be affected by the difference of gut microbiota, thus affecting the taste and nutritional quality.

Characterization of Leishmania Ulcers Microbiota Using Next Generation Sequencing: Leishmania Ulcers Microbiota

The human skin microbiome is a major source of bacteria in cutaneous leishmaniasis (CL) ulcers following the fall of the crust and the subsequent formation of a shallow depression in the epidermis and dermis of the skin. As a result, secondary bacterial infections are frequently observed which impair the healing process. Our study aimed at studying the bacterial communities in CL lesions using next-generation sequencing. A total of 298 patients (178 males and 120 females; median age of 17) presenting ulcerated skin lesions suspected with CL were included in this study. CL was confirmed in 153 (51%) cases by ITS1-PCR and/ or microscopy. Based on bacterial 16S rRNA-PCR, 92 samples were positive for the presence of bacteria, while 206 samples were negative and excluded from the microbiome study. A total of 925 Operational Taxonomic Units (OTUs) were identified and assigned to 215 genera. Despite insignificant difference in the microbiome composition between CL and non-CL lesions, the phylum level analysis revealed that Actinobacteria was significantly higher in CL ulcers while Protoeobacteria was significantly higher in non-CL ulcers (X2, P=0.039). The relative abundance of the most commonly encountered skin pathogens i. e E coli, Pseudomonas aeruginosa, Enterobacter, Enterococcus and Acinetobacter species were significantly higher in non-CL ulcers (X2, P&lt;0.05) compared to Staphylococcus aureus and Proteus mirabilis which were higher in CL ulcers (P&lt;0.05). Our data showed that bacterial communities did not cluster according to the Leishmania infection. Nonetheless, bacterial diversity was lower in CL compared to non-CL lesions. Presence of pathogenic bacteria in CL lesions such as S. aureus might exacerbate lesions, hinder diagnosis, and delay healing.

Autoimmune Hepatitis: Shifts in Gut Microbiota and Metabolic Pathways among Egyptian Patients.

Autoimmune hepatitis (AIH) is a chronic inflammatory disorder with complex immunopathogenesis. Dysbiosis has been linked to many autoimmune diseases, but its detailed role in autoimmune hepatitis (AIH) still needs rigorous evaluation, especially in Egypt. We aimed to identify the shift in the gut microbiota profile and resultant metabolic pathways in AIH Egyptian patients compared to healthy individuals. Stool samples were collected from 15 AIH-naive patients and from 10 healthy individuals. The V3-V4 hyper-variable regions in16S rRNA gene was amplified and sequenced using Illumina MiSeq platform. Significantly lower bacterial diversity in AIH patients was found compared to the controls. A phylum-level analysis showed the overrepresentation of Firmicutes, Bacteroides, and Proteobacteria. At the genus level, AIH-associated enrichment of Faecalibacterium, Blautia, Streptococcus, Haemophilus, Bacteroides, Veillonella, Eubacterium, Lachnospiraceae and Butyricicoccus was reported in contrast to Prevotella, Parabacteroides and Dilaster, which were significantly retracted in such patients. Overall, the predicted metabolic pathways associated with dysbiosis in AIH patients could orchestrate the potential pathogenic roles of gut microbiota in autoimmune disease, though not in a disease-specific manner, calling for future large-scale studies.

The Composition Alteration of Respiratory Microbiota in Lung Cancer

Background: Previous studies have reported mixed results regarding the composition of respiratory microbiota in lung cancer patients. Therefore, relying on previously published studies, we sought to estimate the relative proportion of respiratory microbiota between lung cancer cases and controls.Methods: MEDLINE, Embase, The Cochrane Library, and Web of Science online databases were systematically searched from inception up to October 14, 2019, to retrieve relevant studies. The relative abundance of each predominant taxon of respiratory microbiota in lung cancer patients and controls was pooled using the reported outcome data.Results: A total of 8 studies comprising 530 participants were included in the final analysis. The pooled phylum level analysis revealed that Bacteroidetes and Proteobacteria were the most abundant bacterial phyla among all participants, recording 17.5%, 47.5% in lung cancer patients, 28.2%, 39.27% in patients with benign pulmonary diseases and 40.62%, 32.09% in healthy controls, respectively. In addition, Actinobacteria and Firmicutes phyla were abundant in lung cancer cases compared to other groups (14.8%, 17.62% for lung cancer versus 13.04%, 13.16% for benign pulmonary nodules and 12.43%, 12.45% for healthy controls). At genus level, Prevotella was predominant in all the participants, and its proportion was relatively lower in cancer patients (25.74% for lung cancer versus 35.59% and 36.75% for benign pulmonary nodules and healthy controls, respectively). Comparatively, Streptococcus was more abundant in lung cancer cases (9.65% in lung cancer versus 7.98%, 7.26% in benign pulmonary nodules and healthy controls).Conclusions: The respiratory microbiota composition of respiratory microbiota significantly differs between lung cancer patients and healthy individuals, and may be used as potential biomarker of lung cancer. In addition, larger sample size, standardized procedures, dynamic monitoring, metabolomics, and culturomics are needed to confirm these results.

New Insights on Obesity and Diabetes from Gut Microbiome Alterations in Egyptian Adults

Obesity and diabetes are reaching epidemic levels globally. Metagenomics and microbiome science have recently emerged as new tools for studying common complex human diseases. We report in this study notable differences in gut microbiome in adult patients with obesity and diabetes in Egypt. The experimental design was based on comparisons of four study groups: (1) Controls (C) with a normal body mass index, without obesity or diabetes, (2) Obese adults (O) without diabetes, (3) adults with diabetes (D) who are not obese, and (4) Adults who are both obese and diabetic (OD). In a total study sample of 60 participants, we sequenced the 16S ribosomal RNA (rRNA) gene using the Illumina MiSeq platform. Alpha diversity analysis revealed greater diversity in bacterial communities of (D) than controls. Phylum-level analysis identified a trend for overrepresentation of Bacteroidetes (p < 0.07) in (O) and (D) than controls. The ratio of Firmicutes/Bacteroidetes (F/B) displayed a remarkable increase in (OD) than controls. At genus level, Faecalibacterium (p < 0.05) and Akkermansia (p < 0.001) distinguished (O) from controls, while Fusobacterium (p < 0.001) and Bacteroides (p < 0.001) was significantly more abundant in (OD) compared with D. Surprisingly, isoquinoline, quinone and ubiquinone alkaloid biosynthesis were overrepresented in controls compared with other three study groups. Presumably, the latter observation might potentially suggest an antihyperglycemic activity of the gut microbiota. In conclusion, the health state of the adults in our study defined the composition of the gut microbiota. Moreover, obesity and diabetes were associated with remarkably enriched populations of Firmicutes and Bacteroidetes. The abundance of Fusobacterium is worth further research and exploration as a candidate biomarker for prediabetes especially in obese individuals. The potential antihyperglycemic activity of the gut microbiota is also noteworthy for future studies in other world populations.

The respiratory microbiota: new insights into pulmonary tuberculosis

BackgroundPrevious studies demonstrated that the diversity and composition of respiratory microbiota in TB patients were different from healthy individuals. Therefore, the aim of the present analysis was to estimate the relative proportion of respiratory microbiota at phylum and genus levels among TB cases and healthy controls.MethodsThe PubMed and Google Scholar online databases were searched to retrieve relevant studies for the analysis. The statistical analysis was done using STATA version 11, pooled estimates are presented using graphs. The summary of findings in included studies is also presented in Table 1.ResultsThe phylum level analysis shows that the pooled proportions of Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Crenarchaeota were determined among tuberculosis patients and healthy controls. In brief, Firmicutes, and Proteobacteria were the most abundant bacterial phyla in both TB cases and healthy controls, composing 39.9 and 22.7% in TB cases and 39.4 and 19.5% in healthy controls, respectively. The genus level analysis noted that Streptococcus (35.01%), Neisseria (27.1%), Prevotella (9.02%) and Veillonella (7.8%) were abundant in TB patients. The Prevotella (36.9%), Gammaproteobacteria (22%), Streptococcus (19.2%) and Haemophilus (15.4%) were largely seen in healthy controls. Interestingly, Veillonella, Rothia, Leuconostoc were unique to TB cases, whereas Lactobacillus, and Gammaproteobacteria, Haemophilus, and Actinobacillus were identified only in healthy controls.ConclusionThe composition of the respiratory microbiota in TB patients and healthy controls were quite different. More deep sequencing studies are needed to explore the microbial variation in the respiratory system in connection with TB.

Characteristics of Faecal Microbiota in Korean Patients with Clostridioides difficile-associated Diarrhea.

BackgroundThe intestinal microbiota plays an important role in the pathogenesis of Clostridioides difficile-associated diarrhea, and regional and racial characteristics influence the microbiome composition and diversity. We investigated the intestinal microbiome characteristics of patients with C. difficile colitis (CD+) compared to those of patients with colitis not due to C. difficile (CD−), patients with vancomycin-resistant enterococci (VRE) colonization, and healthy controls, in Korea.Materials and MethodsWe collected stool samples from 24, 18, 11 and 13 subjects within CD+, CD−, VRE and healthy control groups, respectively. The microbial communities were evaluated by 454-pyrosequencing of bacterial 16s rRNA.ResultsThe species richness and microbial diversity were significantly lower in the CD+ group compared to those in healthy controls, but not compared to those in CD− and VRE groups. Phylum-level analysis showed that the proportion of Actinobacteria in the CD+ group was significantly lower than in the healthy control, but was unchanged compared to that in CD− and VRE groups. At the genus level, compared to the healthy group, the CD+ group showed significantly lower proportions of Blautia, Bifidobacterium, Faecalibacterium et al. Compared to the VRE group, the CD+ group showed a significantly higher proportion of Anaerostipes.ConclusionsWe could identify the intestinal microbiome characteristics of Koreans with C. difficile colitis. It might help to develop microbiome based diagnostic and treatment modalities.

Response of macrophyte communities to flow regulation in mountain streams.

River macrophytes are widely used in freshwater ecosystem assessment because of their sensitivity to anthropogenic pressures, even if there are only a few studies that investigated how macrophytes respond to water regime alterations. In this study, we analyzed the effects of dams on river macrophyte communities through a comparison between upstream and downstream sides from 18 dams located in Alps and Apennines. A co-inertia analysis and a Mantel test were applied to assess if the analysis of environmental parameters could be effective in predicting macrophyte community structure. We analyzed morphological and physicochemical inter-site differences and tested the influence of dams on various aspects of community structure (composition, richness, diversity, dominance, coverage) using multivariate randomized block permutation procedure. Plant similarity between sites was evaluated at the level of phylum, and indicator species analysis was performed to identify the taxa most sensitive or tolerant to water regulation. We found that the overall environmental setting overwhelms the dam impact and that the influence of hydrological alteration became apparent when comparing upstream and downstream assemblages at the same dam. In particular, we found that most of taxa had a higher affinity with the downstream side and that in general, stream regulation increases plant richness and coverage, but reduces community evenness. Analyses based on higher taxonomic groups (phyla) demonstrated that this community can be effectively used in bioassessment even at phylum level analysis. In particular, we found that bryophytes, strictly linked with changes in substrate stability, show particular sensitivity to water regulation in mountain streams.

Unique hyper-thermal composting process in Kagoshima City forms distinct bacterial community structures

A unique compost, Satsuma soil, is produced from three types of wastewater sludge using hyper-thermal processes at temperatures much higher than that of general thermophilic processes in Kagoshima City, Japan. We analyzed the bacterial community structures of this hyper-thermal compost sample and other sludges and composts by a high-throughput barcoded pyrosequencing method targeting the 16S rRNA gene. In total, 621,076 reads were derived from 17 samples and filtered. Artificial sequences were deleted and the reads were clustered based on the operational taxonomic units (OTUs) at 97% similarity. Phylum-level analysis of the hyper-thermal compost revealed drastic changes of the sludge structures (each relative abundance) from Firmicutes (average 47.8%), Proteobacteria (average 22.3%), and Bacteroidetes (average 10.1%) to two main phyla including Firmicutes (73.6%) and Actinobacteria (25.0%) with less Proteobacteria (∼0.3%) and Bacteroidetes (∼0.1%). Furthermore, we determined the predominant species (each relative abundance) of the hyper-thermal compost including Firmicutes related to Staphylococcus cohnii (13.8%), Jeotgalicoccus coquinae (8.01%), and Staphylococcus lentus (5.96%), and Actinobacteria related to Corynebacterium stationis (6.41%), and found that these species were not predominant in wastewater sludge. In contrast, we did not observe any common structures among eight other composts produced, using the hyper-thermal composts as the inoculums, under thermophilic conditions from different materials. Principle coordinate analysis of the hyper-thermal compost indicated a large difference in bacterial community structures from material sludge and other composts. These results suggested that a distinct bacterial community structure was formed by hyper-thermal composting.

Microbiome diversity in the sputum of patients with pulmonary tuberculosis.

TB is a worldwide pandemic. India has the highest burden of TB, with WHO statistics for 2013 giving an estimated incidence figure of 2.1 million cases for India out of a global incidence of 9 million. Microbiota have been shown to be associated with many disease conditions; however, only few studies have been reported for microbiota associated with TB infection. For the first time, we characterized the composition of microbiota of TB patients of India, using high-throughput 16S rRNA gene sequencing and compared it with healthy controls. Phylum-level analysis showed that the relative abundance of Firmicutes and Actinobacteria was significantly higher in TB samples and Neisseria and Veillonella were two dominant genera after Streptococcus. In our study, significantly different core genera in TB and normal population were found as compared with the reported studies. Also, the presence of diverse opportunistic pathogenic microbiota in TB patients increases the complexity and diversity of sputum microbiota. Characterization of the sputum microbiome is likely to provide important pathogenic insights into pulmonary tuberculosis.

A novel sub-phylum method discriminates better the impact of crop management on soil microbial community

Soil microorganisms such as mycorrhizae and plant-growth-promoting rhizobacteria have beneficial effects on crop productivity. Agricultural practices are known to impact soil microbial communities, but past studies examining this impact have focused mostly on one or two taxonomic levels, such as phylum and class, thus missing potentially relevant information from lower levels. Therefore, we propose here an original, sub-phylum method for studying how agricultural practices modify microbial communities. This method involves exploiting the available sequence information at the lowest taxonomic level attainable for each operational taxonomic unit. In order to validate this novel method, we assessed microbial community composition using 454 pyrosequencing of 16S and 28S rRNA genes, and then we compared the results with results of a phylum-level analysis. Agricultural practices included conventional tillage, reduced tillage, residue removal, and residue retention. Results show that, at the lowest taxonomic level attainable, tillage is the main factor influencing both bacterial community composition, accounting for 13 % of the variation, and fungal community composition, accounting for 18 % of the variation. On the other hand, phylum-level analysis failed to reveal any effect of soil practice on bacterial community composition and missed the fact that different members of the same phylum responded differently to tillage practice. For instance, the fungal phylum Chytridiomycota showed no impact of soil treatment, while sub-phylum-level analysis revealed an impact of tillage practice on the Chytridiomycota sub-groups Gibberella, which includes a notorious wheat pathogen, and Trichocomaceae. This clearly demonstrates the necessity of exploiting the information obtainable at sub-phylum level when assessing the effects of agricultural practice on microbial communities.

OC-074 The Role of the Fungal Microbiota in the Pathogenesis of De-Novo Paediatric Inflammatory Bowel Disease using next Generation Sequencing

<h3>Introduction</h3> Paediatric Inflammatory bowel disease (IBD) incidence is rising worldwide. Recently the role of the gut microbiota has been recognised as pivotal in disease pathogenesis. IBD microbial studies to date have focused on bacterial diversity assessment in established disease cohorts, with limited studies in treatment naive patients. In contrast to bacteria, the exact role of the colonising fungi and their pathogenic potential has not been fully explored. The aim of the study was to examine candidate fungal triggers at disease onset in children with IBD using pyrosequencing, utilising the Bacteria in Inflammatory bowel disease in Scottish Children Undergoing Investigation before Treatment (BISCUIT) study cohort. <h3>Methods</h3> 128 children undergoing colonoscopy were approached from three Scottish paediatric centres (Aberdeen, Glasgow and Dundee) with 100 ultimately recruited and biopsied; 44 IBD (comprising Crohn’s disease (CD; 29), ulcerative colitis (UC; 13) and IBD-type unspecified (2)), 42 normal colon controls (NCC) and 14 “others”. All IBD patient samples were taken from inflamed tissue. Fungal DNA was amplified on a reduced cohort of 37 recruits (13 CD, 12 UC, 12 NCC) using 18S rDNA primers. Roche 454 Titanium sequencing was conducted by NewGene (Newcastle, UK). Data analysis was performed using QIIME version 1.3.0 workflow. Taxonomy assignment of operational taxonomic units (OTUs) was performed according to ribosomal database project taxonomy. OTU tables were rarefied at 3,000 reads. <h3>Results</h3> Fungal DNA was amplifiable from 7 patient samples, 6 children with a diagnosis of IBD – 4 with CD (BISCUIT1, 31, 62 and 89), 2 children with UC (BISCUIT33 and 104) and 1 NCC (BISCUIT 27). Fungal diversity was assessed in all paediatric samples alongside three adult samples to act as comparison. The adult samples comprised 1 patient with UC (2UC21Aa) and 2 NCC (GH4 and GH9). Phylum level analysis indicated that all fungal sequences belonged to the Ascomycota and Basidiomycota phyla. Control patients contained predominantly Ascomycota sequences ( &gt; 80% of sequences in all patients) whilst 6/7 IBD patients contained exclusively Basidiomycota species. Genus level analysis was undertaken and there was no similarity between fungal profiles from the paediatric and adult samples. <h3>Conclusion</h3> By using robust methodology we have characterised the IBD “fungal microbiota” at diagnosis in children. Based on the current study, it would appear that a distinctly altered fungal species profile is present at IBD disease presentation. Further work should now focus on expanding this study and identifying how to beneficially modify the microbiota using established and novel IBD treatments. <h3>Disclosure of Interest</h3> None Declared

Tu1704 The Role of the Fungal Microbiota in the Pathogenesis of De-Novo Pediatric Inflammatory Bowel Disease Using Next Generation Sequencing

Introduction Paediatric Inflammatory bowel disease (IBD) incidence is rising worldwide. Recently the role of the gut microbiota has been recognised as pivotal in disease pathogenesis. IBD microbial studies to date have focused on bacterial diversity assessment in established disease cohorts, with limited studies in treatment naive patients. In contrast to bacteria, the exact role of the colonising fungi and their pathogenic potential has not been fully explored. The aim of the study was to examine candidate fungal triggers at disease onset in children with IBD using pyrosequencing, utilising the Bacteria in Inflammatory bowel disease in Scottish Children Undergoing Investigation before Treatment (BISCUIT) study cohort. Methods 128 children undergoing colonoscopy were approached from three Scottish paediatric centres (Aberdeen, Glasgow and Dundee) with 100 ultimately recruited and biopsied; 44 IBD (comprising Crohn’s disease (CD; 29), ulcerative colitis (UC; 13) and IBD-type unspecified (2)), 42 normal colon controls (NCC) and 14 “others”. All IBD patient samples were taken from inflamed tissue. Fungal DNA was amplified on a reduced cohort of 37 recruits (13 CD, 12 UC, 12 NCC) using 18S rDNA primers. Roche 454 Titanium sequencing was conducted by NewGene (Newcastle, UK). Data analysis was performed using QIIME version 1.3.0 workflow. Taxonomy assignment of operational taxonomic units (OTUs) was performed according to ribosomal database project taxonomy. OTU tables were rarefied at 3,000 reads. Results Fungal DNA was amplifiable from 7 patient samples, 6 children with a diagnosis of IBD – 4 with CD (BISCUIT1, 31, 62 and 89), 2 children with UC (BISCUIT33 and 104) and 1 NCC (BISCUIT 27). Fungal diversity was assessed in all paediatric samples alongside three adult samples to act as comparison. The adult samples comprised 1 patient with UC (2UC21Aa) and 2 NCC (GH4 and GH9). Phylum level analysis indicated that all fungal sequences belonged to the Ascomycota and Basidiomycota phyla. Control patients contained predominantly Ascomycota sequences ( > 80% of sequences in all patients) whilst 6/7 IBD patients contained exclusively Basidiomycota species. Genus level analysis was undertaken and there was no similarity between fungal profiles from the paediatric and adult samples. Conclusion By using robust methodology we have characterised the IBD “fungal microbiota” at diagnosis in children. Based on the current study, it would appear that a distinctly altered fungal species profile is present at IBD disease presentation. Further work should now focus on expanding this study and identifying how to beneficially modify the microbiota using established and novel IBD treatments. Disclosure of Interest None Declared