16S rRNA High-throughput Sequencing Research Articles

Bilberry pomace in rabbit nutrition: effects on growth performance, apparent digestibility, caecal traits, bacterial community and antioxidant status

Agricultural by-products could be used as alternative raw materials in rabbit nutrition as they have been found to be highly nutritious and low cost feeding sources. The aim of this study was to estimate the nutritive value and potential use of bilberry pomace (BP) for growing rabbits. A total of 144 Grimaud rabbits (35 days old) were allotted to four groups and fed with a diet containing increasing level of BP: BP0 (basal diet), BP5, BP10 and BP15 containing 0, 50, 100 and 150 g/kg respectively. Growth trial lasted 48 days; apparent digestibility was evaluated, starting at 46 days of age, over 4 consecutive days. The nutritive value of BP was measured using the mean digestibility of the experimental diets. At 83 days of age, rabbits were slaughtered: blood, and liver and kidney samples were collected in order to determine the blood parameters and the antioxidant enzyme activities of the tissues. Moreover, caecal content was sampled and gut microbiota assessed by means of amplicon-based high-throughput 16S rRNA sequencing and PCR-denaturing gradient gel electrophoresis. The digestible protein was estimated to 104 g/kg of DM while digestible energy to 9.44 MJ/kg DM for incorporation rate up to 150 g/kg. During the finishing period, average daily feed intake and feed conversion ratio showed linear response to BP increase (P=0.008 and <0.001, respectively). During all the period, both parameters decreased linearly and quadratically with increasing BP inclusion levels (P<0.001) up to 100 g/kg of BP. A significant effect of the antioxidant status was found in the kidneys and liver (P<0.05) where the glutathione peroxidase activity increased as the BP increased. As far as gut microbiota is concerned, BP increased the relative abundance of the Clostridium, Oscillospira, Ruminococcus and Ruminococcaceae species which were clearly associated with the BP inclusion level. In conclusion, BP showed a potential use as an alternative protein and fibre sources for growing rabbits.

The microbiome of Escherichia coli and culture-negative nonsevere clinical mastitis: Characterization and associations with linear score and milk production

Culture-negative and Escherichia coli cases are uncommonly treated in pathogen-based protocols for nonsevere mastitis. High-throughput 16S rRNA sequencing might reveal the presence of other pathogens and can provide information on microbial diversity. The objective was to explore the milk microbiome at the time of the mastitis event (enrollment) and its association with survival in the herd, milk production, and postevent linear score (LS) for cows with clinical mastitis characterized as negative or E. coli by culture. Fifty E. coli-positive and 35 culture-negative samples from cases were enrolled. No cases were treated with antimicrobials. All E. coli-positive quarters were characterized as transient; microbiological culture of samples taken 15 d postmastitis were negative for this organism. However, a difference in α-diversity (Shannon index) was present between enrollment and follow-up samples (3.8 vs. 5.1). When α-diversity was explored for enrollment E. coli samples, no relationship was observed between the Shannon indices of these samples and postmastitis LS. Alpha-diversity of the enrollment samples was lower for E. coli-positive cows that subsequently had greater losses in milk production. This difference was explained by a greater relative abundance of the family Enterobacteriaceae (67.8 vs. 38.4%) for cows that dropped in production. Analysis of composition of the microbiome identified one phylum, Proteobacteria, that differed between E. coli-positive cows that dropped in production and those that did not. Evaluation of β -diversity found no statistical relationship between postmastitis LS and the microbiome. When evaluating α- and β-diversities and composition of the microbiomes for culture-negative quarters, no associations were found for milk production changes and postmastitis LS. Three cows did not remain in the herd, limiting the ability to analyze survival. The findings suggest that a contributing factor to negative outcomes in E. coli-positive cows is relative abundance of this pathogen, and that no single or collective group of bacterial families is associated with milk production changes or postmastitis LS in culture-negative quarters. Although additional studies should be performed, the absence of associations between outcomes explored and microbial profiles in this study suggests that we are not missing opportunities by not treating nonsevere E. coli or culture-negative mastitis cases.

Orally administered gold nanoparticles protect against colitis by attenuating Toll-like receptor 4- and reactive oxygen/nitrogen species-mediated inflammatory responses but could induce gut dysbiosis in mice

BackgroundGold nanoparticles (AuNPs) are attracting interest as potential therapeutic agents to treat inflammatory diseases, but their anti-inflammatory mechanism of action is not clear yet. In addition, the effect of orally administered AuNPs on gut microbiota has been overlooked so far. Here, we evaluated the therapeutic and gut microbiota-modulating effects, as well as the anti-inflammatory paradigm, of AuNPs with three different coatings and five difference sizes in experimental mouse colitis and RAW264.7 macrophages.ResultsCitrate- and polyvinylpyrrolidone (PVP)-stabilized 5-nm AuNPs (Au-5 nm/Citrate and Au-5 nm/PVP) and tannic acid (TA)-stabilized 5-, 10-, 15-, 30- and 60-nm AuNPs were intragastrically administered to C57BL/6 mice daily for 8 days during and after 5-day dextran sodium sulfate exposure. Clinical signs and colon histopathology revealed more marked anti-colitis effects by oral administration of Au-5 nm/Citrate and Au-5 nm/PVP, when compared to TA-stabilized AuNPs. Based on colonic myeloperoxidase activity, colonic and peripheral levels of interleukin-6 and tumor necrosis factor-α, and peripheral counts of leukocyte and lymphocyte, Au-5 nm/Citrate and Au-5 nm/PVP attenuated colonic and systemic inflammation more effectively than TA-stabilized AuNPs. High-throughput sequencing of fecal 16S rRNA indicated that AuNPs could induce gut dysbiosis in mice by decreasing the α-diversity, the Firmicutes/Bacteroidetes ratio, certain short-chain fatty acid-producing bacteria and Lactobacillus. Based on in vitro studies using RAW264.7 cells and electron spin resonance oximetry, AuNPs inhibited lipopolysaccharide (LPS)-triggered inducible nitric oxide (NO) synthase expression and NO production via reduction of Toll-like receptor 4 (TLR4), and attenuated LPS-induced nuclear factor kappa beta activation and proinflammatory cytokine production via both TLR4 reduction and catalytic detoxification of peroxynitrite and hydrogen peroxide.ConclusionsAuNPs have promising potential as anti-inflammatory agents; however, their therapeutic applications via the oral route may have a negative impact on the gut microbiota.

Comparison of intestinal microbes in female and male Chinese concave-eared frogs (Odorrana tormota) and effect of nematode infection on gut bacterial communities.

The Chinese concave‐eared frog (Odorrana tormota) is a rare and threatened species with remarkable sexual dimorphism. Intestinal microbes are understood to play important roles in animal physiology, growth, ecology, and evolution. However, little is known about the intestinal microbes in female and male frogs, as well as the contributing effect by gut infesting nematodes to the co‐habiting bacteria and their function in degradation food rich in chitin. Here, this study analyzed the microbiota of the intestinal tract of both female and male, healthy as well as nematode‐infested concave‐eared frogs using high throughput 16S rRNA sequencing and metagenomic techniques. The results showed that the bacterial composition of the microbiota at the phylum level was dominated by Firmicutes, Verrucomicrobia, Bacteroidetes, and Proteobacteria. The study also revealed that the community composition below the class level could be represent sex differences, particularly with regard to Enterobacteriales, Enterobacteriaceae, Peptostreptococcaceae, and Rikenellaceae, among others. Carbohydrate‐active enzyme‐encoding genes and modules were identified in related gut bacteria by metagenomic analysis, with Bacteroidia, Clostridia, and gammaproteobacteria predicted to be the main classes of chitin‐decomposing bacteria in the frog intestine. In addition, the abundance of some bacteria significantly increased or decreased in nematode‐infected hosts compared with healthy individuals, including Verrucomicrobia, Verrucomicrobiae, Negativicutes, Actinobacteria, and Bacilli, among others. This indicates that nematode infection may affect the richness and composition of some gut bacteria.

Distinct community structure and microbial functions of biofilms colonizing microplastics

Microplastics are frequently detected in freshwater environments, serving as a new factitious substrate for colonization of biofilm-forming microorganisms. Distinct microbial assemblages between microplastics and surrounding waters have been well documented; however, there is insufficient knowledge regarding biofilm colonization of plastic and non-plastic substrates, despite the fact that microbial communities generally aggregate on natural solid surfaces. In this study, the effects of substrate type on microbial communities were evaluated by incubation of biofilms on microplastic substrates (polyethylene and polypropylene) and natural substrates (cobblestone and wood) for 21 days under controlled conditions. Results from high-throughput sequencing of 16S rRNA revealed that the alpha diversity (richness, evenness, and diversity) was lower in the microplastic-associated communities than in those on the natural substrates, indicating substrate-type-coupled species sorting. Distinct community structure and biofilm composition were observed between these two substrate types. Significantly higher abundances of Pirellulaceae, Phycisphaerales, Cyclobacteriaceae, and Roseococcus were observed on the microplastic substrates compared with the natural substrates. Simultaneously, the functional profiles (KEGG) predicted by Tax4Fun showed that the pathways of amino acid metabolism and metabolism of cofactors and vitamins were increased in biofilms on the microplastic substrates. The findings illustrate that microplastic acts as a distinct microbial habitat (compared with natural substrates) that could not only change the community structure but also affect microbial functions, potentially impacting the ecological functions of microbial communities in aquatic ecosystems.

The gut of the finch: uniqueness of the gut microbiome of the Gal\xe1pagos vampire finch

BackgroundDarwin’s finches are a clade of 19 species of passerine birds native to the Galápagos Islands, whose biogeography, specialized beak morphologies, and dietary choices—ranging from seeds to blood—make them a classic example of adaptive radiation. While these iconic birds have been intensely studied, the composition of their gut microbiome and the factors influencing it, including host species, diet, and biogeography, has not yet been explored.ResultsWe characterized the microbial community associated with 12 species of Darwin’s finches using high-throughput 16S rRNA sequencing of fecal samples from 114 individuals across nine islands, including the unusual blood-feeding vampire finch (Geospiza septentrionalis) from Darwin and Wolf Islands. The phylum-level core gut microbiome for Darwin’s finches included the Firmicutes, Gammaproteobacteria, and Actinobacteria, with members of the Bacteroidetes at conspicuously low abundance. The gut microbiome was surprisingly well conserved across the diversity of finch species, with one exception—the vampire finch—which harbored bacteria that were either absent or extremely rare in other finches, including Fusobacterium, Cetobacterium, Ureaplasma, Mucispirillum, Campylobacter, and various members of the Clostridia—bacteria known from the guts of carnivorous birds and reptiles. Complementary stable isotope analysis of feathers revealed exceptionally high δ15N isotope values in the vampire finch, resembling top marine predators. The Galápagos archipelago is also known for extreme wet and dry seasons, and we observed a significant seasonal shift in the gut microbial community of five additional finch species sampled during both seasons.ConclusionsThis study demonstrates the overall conservatism of the finch gut microbiome over short (< 1 Ma) divergence timescales, except in the most extreme case of dietary specialization, and elevates the evolutionary importance of seasonal shifts in driving not only species adaptation, but also gut microbiome composition.

Characterization of the Microbial Population Inhabiting a Solar Saltern Pond of the Odiel Marshlands (SW Spain)

The solar salterns located in the Odiel marshlands, in southwest Spain, are an excellent example of a hypersaline environment inhabited by microbial populations specialized in thriving under conditions of high salinity, which remains poorly explored. Traditional culture-dependent taxonomic studies have usually under-estimated the biodiversity in saline environments due to the difficulties that many of these species have to grow at laboratory conditions. Here we compare two molecular methods to profile the microbial population present in the Odiel saltern hypersaline water ponds (33% salinity). On the one hand, the construction and characterization of two clone PCR amplified-16S rRNA libraries, and on the other, a high throughput 16S rRNA sequencing approach based on the Illumina MiSeq platform. The results reveal that both methods are comparable for the estimation of major genera, although massive sequencing provides more information about the less abundant ones. The obtained data indicate that Salinibacter ruber is the most abundant genus, followed by the archaea genera, Halorubrum and Haloquadratum. However, more than 100 additional species can be detected by Next Generation Sequencing (NGS). In addition, a preliminary study to test the biotechnological applications of this microbial population, based on its ability to produce and excrete haloenzymes, is shown.

Sponge-microbe partnerships are stable under eutrophication pressure from mariculture

Sponges harbor a great diversity of symbiotic microorganisms. However, environmental stresses can affect this partnership and influence the health and abundance of the host sponges. In Bolinao, Pangasinan, Philippines, chronic input of organic materials from mariculture activities contributes to a eutrophic coastal environment. To understand how these conditions might affect sponge-microbial partnerships, transplantation experiments were conducted with the marine sponge Gelliodes obtusa. High-throughput sequencing of 16S rRNA revealed that the associated microbial community of the sponges did not exhibit significant shifts after six weeks of transplantation at a eutrophic fish farm site compared to sponges grown at a coral reef or a seagrass area. However, sponges at the fish farm revealed higher abundance of the amoA gene, suggesting that microbiome members are responsive to increased ammonium levels at the site. The stable association between G. obtusa and its microbiome indicates that the sponge holobiont can withstand eutrophication pressure from mariculture.

Changes of the organic carbon content and stability of soil aggregates affected by soil bacterial community after afforestation

Soil aggregation is one of the most important factors affecting soil organic carbon (SOC) stabilization, and the stability of aggregates depends in part on soil microbial diversity and composition. Interactions between the soil bacterial community and SOC content in soil aggregates after afforestation are poorly understood. In this study, we investigated difference in the diversity of soil bacterial with high-throughput 16S rRNA sequencing, as well as the SOC content in soil aggregates representing a chronosequence of 42, 27, and 17 years of Robinia pseudoacacia L. succession (RP42, RP27, and RP17), and in farmland (FL) soil for comparison (millet (Setaria italica) and soybean (Glycine max) rotation).The SOC content in RP17, RP27, and RP42 plots were significantly higher than that of FL by an average of 85.57%, 142.37%, and 76.69% in large macro-aggregates (>1 mm), small macro-aggregates (0.25–1 mm), and micro-aggregates (<0.25 mm), respectively. The Simpson index for the FL plot was significantly higher than that of the RP17, RP27, and RP42 plots, whereas the Shannon index followed the opposite trend. The dominant bacterial phyla detected were Proteobacteria, Acidobacteria, and Actinobacteria in each afforested and FL sites. These data revealed significant correlations between soil aggregate characteristics, such as SOC content, mean weight diameter (MWD), and geometric mean diameter (GMD), with the relative abundance of Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, Verrucomicrobia, and Planctomycetes. These relationships suggested that the effects of afforestation on SOC stabilization in soil aggregates are modulated by both soil aggregate size and also soil bacterial diversity. We demonstrate that the interaction between soil aggregate size and soil microbes might be a key factor in effective soil conservation, restoration, sustainability of agroecosystems, and erosion prevention.

Application of Bioaugmentation Technology in Cold-Rolling Emulsion Wastewater Treatment and Analysis of Microbial Community

Cold-rolling emulsion wastewater (CREW) is characterized by high oil content, complex organic components and certain toxicity. By traditional physical and chemical methods, it could not be completely degraded at low cost. In order to optimize treatment process of CREW, a highly effective strain (Pseudomonas fluorescens) was isolated and combined with bioaugmentation technology, biofilm and fluidized bed technology to treat CREW. After 78 days of the system operation, the removal rate of COD and oil reached 94% and 97%. COD and oil content of the effluent were stably below 70mg/L and 4.7mg/L, which met the first order of the national discharge standard (GB8978-1996). The result of high throughput 16SrRNA sequencing showed there were 23 genera of bacteria in the biofilm community of the reactor. This microbial community structure could effectively degrade COD and oil in CREW. At phylum level, γ-proteobacteria, Firmicutes and β-proteobacteria widely existed in carrier and were the main members of pollutant degradation.

Phylogenetically distinct methanotrophs modulate methane oxidation in rice paddies across Taiwan

Rice paddies are considerable sources of methane because of the highly reduced soil oxidation–reduction conditions during rice cultivation. In this ecosystem, active methane-oxidizing bacteria are important, because they consume methane while reducing the overall emissions from rice paddy soils. However, the biogeographic distribution of active methanotrophs in paddy soils across Taiwan remains poorly understood. We used DNA-based stable isotope probing (DNA-SIP) to show that phylogenetically distinct type I and type II methanotrophs dominated methane oxidation in geographically different paddy soils across Taiwan. High-throughput sequencing of soil 16S rRNA and pmoA genes under field conditions revealed that a type II methanotroph, Methylocystis, was predominant in rice paddy soils. In addition, an uncultured novel type I methanotroph cluster (Rice Paddy Clusters) was detected with the closest relatedness to Methylocaldum 16S rRNA genes in all rice field soils tested. SIP microcosm incubation, however, suggested that the type I methanotrophs Methylosarcina and Methylobacter were significantly stimulated during the consumption of high-concentration methane in five paddy soils with pH > 6.07, whereas the Methylosinus-like microorganisms of type II methanotrophs dominated aerobic methane-oxidizing communities in acidic soil with pH = 5.17. Furthermore, high-throughput sequencing of 13C-pmoA genes indicated the presence of novel methanotrophs that are phylogenetically distantly related to the type I methanotrophs Methylosarcina in four out of five non-acidic paddy soils studied, and the high proportions in the 13C-DNA suggested that these uncultured methanotrophs play an important role in methane oxidation. These results provide strong evidence for the environmental selection of phylogenetically distinct methanotrophs under field conditions. Moreover, community shifts in active methanotrophs likely occurred in response to environmental variations with fluctuating methane concentrations.

Dynamics and diversity of microbial community succession during fermentation of Suan yu, a Chinese traditional fermented fish, determined by high throughput sequencing

The main goal of this study was to investigate the dynamics, diversity and succession of microbial community present during the preparation of Suan yu (fermented fish), with and without starter cultures by high-throughput sequencing of 16S rRNA and ITS1 genes. Firmicutes and Ascomycota were the predominant phyla of bacteria and fungi, respectively, in all samples. At the genus level, Lactobacillus, Macrococcus and Staphylococcus were the predominating bacteria throughout the fermentation process, regardless of the inclusion of starter cultures. Saccharomyces was the predominating fungal genus in the early-fermentation stage of samples that inoculated starter cultures (MS), while the final product was dominated by Candida and Wickerhamomyces. Compared with naturally-fermented samples (NS; no starter cultures), Lactococcus, Leuconostoc, Enterococcus, Vibrio, Fusicolla and Torulaspora were inhibited and Aureobasidium emerged in samples inoculated with starter cultures (P < .05). Unweighted pair-group and principal component analyses of bacterial and fungal compositions revealed that microbiota structures differed between NS and MS samples. Redundancy analysis indicated that water content and pH might be important factors influencing the dominant bacterial and fungal community. Results indicated that microbial community were dynamic during fermentation process and the inoculation of mixed starter culture inhibited the growth of many organisms associated with food spoilage and contributed to the improvement of the quality of Suan yu products.

Characterization of the Microbiota in Air- or Vacuum-Packed Crisp Grass Carp (Ctenopharyngodon idella C. et V.) Fillets by 16S rRNA PCR–Denaturing Gradient Gel Electrophoresis and High-Throughput Sequencing

The microbial communities in air- and vacuum-packed crisp grass carp ( Ctenopharyngodon idella C. et V.) fillets have not been characterized during chilled storage. High-throughput sequencing of bacterial 16S rRNA has now revealed that the bacterial community in fresh fillets is diverse and distinct from that in spoiled samples. The predominant phylum was Proteobacteria, and 66 genera were identified. In fresh fillets, the most abundant genera were Acinetobacter (53.3%), Wautersiella (6.3%), unclassified Alcaligenaceae (4.4%), Stenotrophomonas (3.8%), unclassified Enterobacteriaceae (3.8%), and Enhydrobacter (3.6%). These genera diminished during chilled storage and sometimes disappeared. At the end of storage, Aeromonas and Pseudomonas were the most abundant. Similar results were obtained by PCR-denaturing gradient gel electrophoresis. These data provide detailed insight into the evolving bacterial communities in air- and vacuum-packed crisp grass carp fillets during storage, revealing Aeromonas and Pseudomonas as major spoilage organisms. These data may be useful for improvement of crisp grass carp quality and shelf life during chilled storage.

Chronic rhinosinusitis with nasal polyps is characterized by dysbacteriosis of the nasal microbiota

Chronic rhinosinusitis with nasal polyp (CRSwNP) patients are often characterized by asthma comorbidity and a type-2 inflammation of the sinonasal mucosa. The mucosal microbiota has been suggested to be implicated in the persistence of inflammation, but associations have not been well defined. To compare the bacterial communities of healthy subjects with CRSwNP patients, we collected nasal swabs from 17 healthy subjects, 21 CRSwNP patients without asthma (CRSwNP−A), and 20 CRSwNP patients with co-morbid asthma (CRSwNP+A). We analysed the microbiota using high-throughput sequencing of the bacterial 16S rRNA. Bacterial communities were different between the three groups. Haemophilus influenzae was significantly enriched in CRSwNP patients, Propionibacterium acnes in the healthy group; Staphylococcus aureus was abundant in the CRSwNP−A group, even though present in 57% of patients. Escherichia coli was found in high amounts in CRSwNP+A patients. Nasal tissues of CRSwNP+A patients expressed significantly higher concentrations of IgE, SE-IgE, and IL-5 compared to those of CRSwNP−A patients. Co-cultivation demonstrated that P. acnes growth was inhibited by H. influenzae, E. coli and S. aureus. The nasal microbiota of healthy subjects are different from those of CRSwNP−A and CRSwNP+A patients. However, the most abundant species in healthy status could not inhibit those in CRSwNP disease.

Microbial community structure and distribution in the air of a powdered infant formula factory based on cultivation and high-throughput sequence methods

The air in a powdered infant formula (PIF) factory is a potential transfer medium for microorganisms. In this study, air samples from 6 main processing areas, almost covering the whole PIF processing line and 1 outdoor location, were collected from a PIF manufacturing plant during the winter and summer periods. A cultivation-based and an Illumina (San Diego, CA) high-throughput 16S rRNA sequencing method was used to investigate the community structures and distributions of bacteria in the air. High microbial diversity (25 genera, 56 species), with a dominant community including Staphylococcus, Bacillus, Acinetobacter, and Kocuria, was found by the cultivation-based method. Moreover, 104 genera were obtained from all samples by high-throughput sequencing methods. Lactococcus (32.3%), Bacillus (29.6%), and Staphylococcus (14.0%) were the preponderant genera. The indices from high-throughput sequencing results indicated that the bacterial community of the air samples was highly diverse. Significant differences in the diversity and distribution at 6 sampling locations were revealed using the 2 methods. In particular, the packaging process contained the highest proportion (39.4%) of isolated strains. The highest diversity in bacterial community structure was found in the outdoor location. More bacterial isolates and higher community diversity were observed in the summer samples compared with the winter samples. In addition, some pathogens, such as Acinetobacter baumannii, Bacillus cereus, and Staphylococcus cohnii, were mainly found in the large bag filling process, can filling, and packaging process areas. The present study provides greater insight into the microbial community and identifies potential sources of air contamination in PIF production environments and can serve as a guide to reduce the risk of microbial contamination in the production of PIF.

Gut commensal-dependent production of autoantibodies against the primordial lupus autoantigen Ro60 in the absence of mammalian Ro60.

Abstract Introduction The RNA-binding protein Ro60 is a primordial autoantigen in systemic lupus erythematosus (SLE), which is highly conserved across multiple species. We have previously linked anti-human Ro60 T cell and antibody responses to human commensals carrying Ro60 orthologs. Here, we tested in vivo if these autoantibodies can arise due to the murine gut microbiota in the absence of host Ro60 protein. Methods Lupus-prone TLR7 tg B6 mice were crossed to Ro60 KO B6 mice and followed longitudinally for Ro60 IgG ELISAs. Littermates were treated with broad-spectrum antibiotics (vancomycin, neomycin, ampicillin, metronidazole) to determine if depletion of the gut microbiota affects anti-Ro60 autoantibody induction and disease manifestations. High-throughput 16S rRNA sequencing of the V4 region was performed on the MiSeq platform. Results TLR7 tg mice produced persistently anti-Ro60 autoantibodies despite crossing to Ro60 KO mice. Oral administration of antibiotics significantly lowered anti-Ro60 autoantibodies (n=6 each, p=0.007). 16S sequencing of antibiotics-fed mice demonstrated outgrowth of Streptophyta but suppression of taxa that may contain commensal Ro60 orthologs (Clostridiaceae, Bacteroides). Conclusions Mice genetically prone to SLE-like disease can mount autoimmune responses against Ro60 even in the absence of the autoantigen. These findings suggest an antigenic trigger within the microbiota, which is supported by interventional studies with antibiotics and 16S sequencing. In summary, these studies suggest a mechanism for the development of lupus which extends beyond the known traditional risk factors.

MicroRNA-146a Deficiency Protects against Listeria monocytogenes Infection by Modulating the Gut Microbiota.

The gut microbiota and microRNAs play important roles in the defense against infection. However, the role of miR-146a in L. monocytogenes infection and gut microbiota remains unclear. We tried to determine whether miR-146a controlled L. monocytogenes infection by regulating the gut microbiota. Wild-type and miR-146a-deficient mice or macrophages were used to characterize the impact of miR-146a on animal survival, cell death, bacterial clearance, and gut microbiota following L. monocytogenes challenge. We found that L. monocytogenes infection induced miR-146a expression both in vitro and in vivo. When compared to wild-type mice, miR-146a-deficient mice were more resistant to L. monocytogenes infection. MiR-146a deficiency in macrophages resulted in reduced invasion and intracellular survival of L. monocytogenes. High-throughput sequencing of 16S rRNA revealed that the gut microbiota composition differed between miR-146a-deficient and wild-type mice. Relative to wild-type mice, miR-146a-deficient mice had decreased levels of the Proteobacteria phylum, Prevotellaceae family, and Parasutterella genus, and significantly increased short-chain fatty acid producing bacteria, including the genera Alistipes, Blautia, Coprococcus_1, and Ruminococcus_1. Wild-type mice co-housed with miR-146a-deficient mice had increased resistance to L. monocytogenes, indicating that miR-146a deficiency guides the gut microbiota to alleviate infection. Together, these results suggest that miR-146a deficiency protects against L. monocytogenes infection by regulating the gut microbiota.

Bacterial community diversity in a full scale biofilter treating wastewater odor.

Constantly, the odors coming from sewage plants are considered a problem by the population. The purpose of this study was to evaluate the microbial community present in a full scale biofilter used for odor treatment. The filter was packed with peat. The main gas treated was hydrogen sulphide (H2S). The removal efficiency reached 99%, with an empty bed residence time of 30 seconds. Molecular analysis can enhance our understanding of the microbial communities in biofilters treating wastewater odor. The analysis made to characterize microbial community was High-throughput 16S rRNA sequencing analysis MiSeq® Illumina. The sampling, carried out in the year 2015, was seasonal (summer and winter) and spatial (depth and position in the biofilter). In this study, a total of 206,174 raw sequence reads for six samples were analyzed using Mothur software (v 1.33.3) based on MiSeq SOP protocol. After Mothur analysis, the results of the bacterial community were explored at the Phylum and Genus levels. In this study, the efficiency removal of hydrogen sulfide reached values greater than 99% during the monitoring, and the main bacterial genera found were Acidotermus, Telmatobacter, Methylovirgula and Bryobacter representing the bacterial community active in the transformation of H2S into a system with long operating time.

Thermophilic versus mesophilic dark fermentation in xylose-fed fluidised bed reactors: Biohydrogen production and active microbial community

Dark fermentative biohydrogen production in a thermophilic, xylose-fed (50 mM) fluidised bed reactor (FBR) was evaluated in the temperature range 55–70 °C with 5-degree increments and compared with a mesophilic FBR operated constantly at 37 °C. A significantly higher (p = 0.05) H2 yield was obtained in the thermophilic FBR, which stabilised at about 1.2 mol H2 mol−1 xylose (36% of the theoretical maximum) at 55 and 70 °C, and at 0.8 mol H2 mol−1 xylose at 60 and 65 °C, compared to the mesophilic FBR (0.5 mol H2 mol−1 xylose). High-throughput sequencing of the reverse-transcribed 16S rRNA, done for the first time on biohydrogen producing reactors, indicated that Thermoanaerobacterium was the prevalent active microorganism in the thermophilic FBR, regardless of the operating temperature. The active microbial community in the mesophilic FBR was mainly composed of Clostridium and Ruminiclostridium at 37 °C. Thermophilic dark fermentation was shown to be suitable for treatment of high temperature, xylose-containing wastewaters, as it resulted in a higher energy output compared to the mesophilic counterpart.

Activating biochar by manipulating the bacterial and fungal microbiome through pre-conditioning.

Biochar can enhance plant growth and reduce diseases, but frequently the optimal doses for these two benefits do not coincide. An approach is needed that will extend the range of biochar doses resulting in a concurrence of maximum benefits for both plant productivity and disease suppression. A biochar-amended growth medium was pre-conditioned by pre-planting fertigation in order to enhance the indigenous microbial community structure and activity. Cucumber plant performance and resistance against damping-off caused by Pythium aphanidermatum were monitored. Soil microbial activity, as well as bacterial and fungal community structure, were assessed by high-throughput 16S rRNA and ITS1 gene amplicon sequencing. Pre-conditioning enhanced the efficacy of biochar for improving plant performance and suppressing soilborne disease through enriching the medium in beneficial soil microorganisms, increasing microbial and fungal diversity and activity, and eliminating biochar phytotoxic compounds. The pre-conditioning process brought dose-response curves for both growth and disease resistance into sync, resulting in maximum benefits for both. These findings suggest that pre-conditioning should be incorporated as an important stage during biochar application in soil and soilless media.