Members Of Bacteroidetes Research Articles

Degradation of complex arabinoxylans by human colonic Bacteroidetes

Some Bacteroidetes and other human colonic bacteria can degrade arabinoxylans, common polysaccharides found in dietary fiber. Previous work has identified gene clusters (polysaccharide-utilization loci, PULs) for degradation of simple arabinoxylans. However, the degradation of complex arabinoxylans (containing side chains such as ferulic acid, a phenolic compound) is poorly understood. Here, we identify a PUL that encodes multiple esterases for degradation of complex arabinoxylans in Bacteroides species. The PUL is specifically upregulated in the presence of complex arabinoxylans. We characterize some of the esterases biochemically and structurally, and show that they release ferulic acid from complex arabinoxylans. Growth of four different colonic Bacteroidetes members, including Bacteroides intestinalis, on complex arabinoxylans results in accumulation of ferulic acid, a compound known to have antioxidative and immunomodulatory properties.

Dynamic bacterial assembly driven by Streptomyces griseorubens JSD-1 inoculants correspond to composting performance in swine manure and rice straw co-composting

The effect of Streptomyces griseorubens JSD-1 inoculant on composting performance and bacterial community assembly during the swine manure and rice straw co-composting was studied by a high-throughput pyrosequencing technology. The JSD-1 inoculant contributed to a higher temperature (maximum 66.8 °C), a longer thermophilic phase (46 days), and a lower bacterial diversity in JSD-1 compost. The principle component analysis confirmed that JSD-1 inoculant significantly reshaped the microbial communities. The difference in genera significantly increased during both composting processes. The predominant biomarkers were members of Bacteroidetes in JSD-1 composting. The network analysis also showed different chief “connecting” genera in both composts. Moreover, JSD-1 inoculant increased the total nitrogen, phosphorus, and potassium content in composts. The redundancy analysis showed that the bacterial community was mainly influenced by temperature; additionally, the nutrient contents were positively correlated with temperature. These results demonstrated that JSD-1 inoculant drove the bacterial assembly to induce physicochemical property changes in co-composting.

Cross-omics analysis revealed gut microbiome-related metabolic pathways underlying atherosclerosis development after antibiotics treatment

ObjectiveThe metabolic influence of gut microbiota plays a pivotal role in the pathogenesis of cardiometabolic diseases. Antibiotics affect intestinal bacterial diversity, and long-term usage has been identified as an independent risk factor for atherosclerosis-driven events. The aim of this study was to explore the interaction between gut dysbiosis by antibiotics and metabolic pathways with the impact on atherosclerosis development. MethodsWe combined oral antibiotics with different diets in an Apolipoprotein E-knockout mouse model linking gut microbiota to atherosclerotic lesion development via an integrative cross-omics approach including serum metabolomics and cecal 16S rRNA targeted metagenomic sequencing. We further investigated patients with carotid atherosclerosis compared to control subjects with comparable cardiovascular risk. ResultsHere, we show that increased atherosclerosis by antibiotics was connected to a loss of intestinal diversity and alterations of microbial metabolic functional capacity with a major impact on the host serum metabolome. Pathways that were modulated by antibiotics and connected to atherosclerosis included diminished tryptophan and disturbed lipid metabolism. These pathways were related to the reduction of certain members of Bacteroidetes and Clostridia by antibiotics in the gut. Patients with atherosclerosis presented a similar metabolic signature as those induced by antibiotics in our mouse model. ConclusionTaken together, this work provides insights into the complex interaction between intestinal microbiota and host metabolism. Our data highlight that detrimental effects of antibiotics on the gut flora are connected to a pro-atherogenic metabolic phenotype beyond classical risk factors.

Hypertension Is Associated With Intestinal Microbiota Dysbiosis and Inflammation in a Brazilian Population.

Hypertension is a major global health challenge, as it represents the main risk factor for stroke and cardiovascular disease. It is a multifactorial clinical condition characterized by high and sustained levels of blood pressure, likely resulting from a complex interplay of endogenous and environmental factors. The gut microbiota has been strongly supposed to be involved but its role in hypertension is still poorly understood. In an attempt to fill this gap, here we characterized the microbial composition of fecal samples from 48 hypertensive and 32 normotensive Brazilian individuals by next-generation sequencing of the 16S rRNA gene. In addition, the cytokine production of peripheral blood samples was investigated to build an immunological profile of these individuals. We identified a dysbiosis of the intestinal microbiota in hypertensive subjects, featured by reduced biodiversity and distinct bacterial signatures compared with the normotensive counterpart. Along with a reduction in Bacteroidetes members, hypertensive individuals were indeed mainly characterized by increased proportions of Lactobacillus and Akkermansia while decreased relative abundances of well-known butyrate-producing commensals, including Roseburia and Faecalibacterium within the Lachnospiraceae and Ruminococcaceae families. We also observed an inflamed immune profile in hypertensive individuals with an increase in TNF/IFN-γ ratio, and in TNF and IL-6 production when compared to normotensive ones. Our work provides the first evidence of association of hypertension with altered gut microbiota and inflammation in a Brazilian population. While lending support to the existence of potential microbial signatures of hypertension, likely to be robust to age and geography, our findings point to largely neglected bacteria as potential contributors to intestinal homeostasis loss and emphasize the high vulnerability of hypertensive individuals to inflammation-related disorders.

Development and Diversity of Bacterial Biofilms in Response to Internal Tides, a Case Study off the Coast of Kuwait

Information pertaining to changes in abundance and composition of microbial communities on offshore platforms in relation to changes in environmental conditions due to internal tides are scarce. In this study, artificial substrata were deployed at two locations on a gently sloping seabed off the coast of Kuwait. The abiotic factors at the two sites were recorded spatially and temporally using time-series measurements and continuous turbulence profiling for 13 days. Results showed variations in water density between the upper and deeper waters with the pycnocline undulating between 6 and 15 m depth at both locations. In the water layer beneath the pycnocline, significant current shear due to the internal tides led to higher turbidity coupled with lower dissolved oxygen (DO) and chlorophyll a concentration. The microbiological data showed a significant decrease in the biofilm total biomass, bacterial counts and phototrophic biomass with increase in depth at both locations. The 16S rRNA amplicon sequence non-metric multidimensional (NMDS) scaling analysis revealed that biofouling bacterial communities affected by depth with Alphaproteobacteriaand Bacteroidetes members dominated upper and deeper water at both locations. The based-ordination analysis revealed that biofouling bacterial communities at 3 m were different than at 15 m, with a percentage of shared Operational taxonomic units (OTUs) ≤64% between locations and between depths. Despite the limitations of the study, the power of the employed system is demonstrated in the results that shed light on the significance of prevailing environmental conditions associated with internal tides in shaping the biofilm community in subtropical offshore water systems.

Soil microbial community responses to labile organic carbon fractions in relation to soil type and land use along a climate gradient

There has been a growing interest in studying the labile C pool in order to promote the sequestration and stabilization of soil organic carbon (SOC). Although labile SOC fractions have emerged as standardized indicators because of their potential to detect early SOC trends over time, the relationships between microbial attributes and labile SOC remains poorly understood. In this study, we explored the influence of labile SOC fractions on the topsoil bacteria-archaea community across 28 sites with different land use, climate aridity, and soil types across a wide range of SOC content (0.6–12%) in central Chile. We applied Illumina sequencing to the 16S rRNA to examine shifts in the diversity and composition of these soil microbial communities. Additionally, labile SOC fractions such as the permanganate oxidizable carbon (POXC) and light fraction organic matter (LFOM), along with the soil physicochemical properties were analyzed. The results demonstrated that among all of the environmental factors tested, the pH, POXC/SOC ratio and LFOM were key drivers of microbial community structure (β-diversity). The α-diversity metrics exhibited a decreasing trend when aridity increased, and community structure was found to vary, with high POXC/SOC in sites associated with drier conditions. In addition, POXC/SOC ratios and LFOM were clearly related to shifts in the relative abundances of specific taxonomic groups at genera level. When there was high POXC/SOC and low LFOM content, members of Bacteroidetes (Adhaeribacter, Flavisolibacter, and Niastella), Proteobacteria (Skermanella, Ramlibacter, and Sphingomonas), and Archaea (Thaumarchaeota) were found to be the most dominant groups; however, the microbial taxa responded differently to both labile C fraction types. These results have implications for understanding how labile C content can potentially be used to predict shifts in the microbial community, thus facilitating the development of predictive ecosystem models, as well as early warning indicators for soil degradation.

Yak rumen microbial diversity at different forage growth stages of an alpine meadow on the Qinghai-Tibet Plateau.

The rumen microbiota of ruminants plays a vital role in fiber digestion, and environmental factors affect its community structure. The yak (Bos grunniens) is the main livestock species that inhabits the Qinghai-Tibet Plateau (QTP) at regions located at high-altitude of 3,000–5,000 m. This work investigated the rumen bacterial community of yak that grazed on the QTP during the whole year to evaluate the relationship between the rumen bacterial community and the nutrient composition of forage plant at three stages. In this study, the diversity of the rumen prokaryotic community composition was monitored in 10 full-grazing yak in an alpine meadow of the QTP. The nutrient composition of three forage growth stages was determined: re-green stage (REGY), grassy stage (GY), and withered stage (WGY). High-throughput sequencing of bacterial 16S rRNA gene was used. The results showed that the nutritive composition of the alpine meadow changed with the seasons: crude protein (CP) (13.22%) was high in forage during REGY (spring), while neutral detergent fiber (NDF) (59.00%) was high during WGY (winter). Microbial diversity and richness were highest during REGY and the average number of operational taxonomic units from 30 samples was 4,470. The microbial composition was dominated by members of Bacteroidetes (51.82%), followed by Firmicutes (34.08%), and the relative microbial abundance changed in the three forage growth stages. Unweighted UniFrac distance PcoA showed that the bacterial community structure differed between REGY, GY, and WGY. Furthermore, taxonomic groups did not present differences regarding gender in these three stages. The rumen microbiota was enriched with functional potentials that were related to ABC transporters, the two-component system, Aminoacyl-tRNA biosynthesis, and metabolism of Purine, Pyrimidine, Starch and sucrose metabolism. Significant differences were found in the composition, diversity, and function of yak ruminal microorganisms during different forage growth stages. This indicates that microbial changes in the rumen depend on changes in the forage nutritional composition. These findings provide evidence on the rumen microbial diversity of yaks in the QTP.

Durable Long-Term Bacterial Engraftment following Encapsulated Fecal Microbiota Transplantation To Treat Clostridium difficile Infection.

Fecal microbiota transplantation (FMT) has become a common rescue therapy for recurrent Clostridium difficile infection, and encapsulated delivery (cFMT) of healthy donor microbiota shows similar clinical efficacy as more traditional routes of administration. In this study, we characterized long-term patterns of bacterial engraftment in a cohort of 18 patients, who received capsules from one of three donors, up to 409 days post-FMT. Bacterial communities were characterized using Illumina sequencing of the V5-V6 hypervariable regions of the 16S rRNA gene, and engraftment was determined by using the Bayesian algorithm SourceTracker. All patients recovered clinically and were free of C. difficile infection following cFMT. The majority of patients (61%) showed high levels of engraftment after the first week following FMT, which were sustained throughout the year. A small subset, 22%, experienced a decline in donor engraftment after approximately 1 month, and a few patients (17%), two of whom were taking metformin, showed delayed and low levels of donor engraftment. Members of the genera Bacteroides, Parabacteroides, and Faecalibacterium were significantly and positively correlated with donor similarity (ρ = 0.237 to 0.373, P ≤ 0.017). Furthermore, throughout the year, patient fecal communities showed significant separation based on the donor fecal microbiota that they received (P < 0.001). Results of this study, which characterize long-term engraftment following cFMT, suggest that numerical donor similarity is not strictly related to clinical outcome and identify a persistent donor-specific effect on patient fecal microbial communities. Furthermore, results suggest that members of the Bacteroidetes may be important targets to improve engraftment via cFMT.IMPORTANCE Recurrent Clostridium difficile infection (rCDI) is the most common cause of hospital- and community-acquired diarrheal infection associated with antibiotic use. Fecal microbiota transplantation (FMT), a treatment that involves administration of fecal bacteria from a healthy donor to a recipient patient, is a highly effective rescue therapy for rCDI that is increasingly being incorporated into standard clinical practice. Encapsulated, freeze-dried preparations of fecal microbiota, administered orally, offer the simplest and most convenient route of FMT delivery for patients (cFMT). In this study, we evaluated the extent of bacterial engraftment following cFMT and the duration of donor bacterial persistence. All patients studied recovered clinically but showed differing patterns in long-term microbial community similarity to the donor that were associated with members of the bacterial group Bacteroidetes, previously shown to be prominent contributors to rCDI resistance. Results highlight long-lasting, donor-specific effects on recipient patient microbiota and reveal potential bacterial targets to improve cFMT engraftment.

Biochar Amendment Stimulates Utilization of Plant-Derived Carbon by Soil Bacteria in an Intercropping System.

Plant-derived carbon (C) is considered fundamental to understand the interaction between rhizosphere microbes and plants in terrestrial ecosystems. Biochar soil amendment may enhance plant performance via changing soil properties or microbial diversity in the rhizosphere. However, our knowledge of how plant-microbiome associations respond to biochar amendment remains rather limited. Herein, 13CO2 steady-state labeling combined with DNA stable-isotope probing was used to characterize soil bacterial communities in the rhizosphere contributing to the utilization of plant-derived C. The diversity of bacteria active in the utilization of root exudates was determined after biochar amendment in a legume-based intercropping system (Vicia faba L., with Zea mays L.). The results showed the biochar application not only changed the bacterial community structure and diversity in the rhizosphere, but also altered bacterial members actively assimilating plant-derived C. There were more labeled species in the biochar-amended soils than the control soils. Compared with the control, the biochar amendment increased the relative abundances of Firmicutes and Bacteroidetes members (i.e., Bacillus, Clostridium, Sporomusa, Desulfosporosinus, and Alicyclobacillus) while decreasing the abundances of Proteobacteria members (e.g., Methylobacterium and Sphingomonas) utilizing plant-derived C. In contrast, slow-growing species of the phyla Acidobacteria, Planctomycetes, and Gemmatimonadetes were barely labeled. The bacteria found stimulated by the biochar amendment are known for their ability to fix nitrogen, solubilize phosphorus, or reduce iron and sulfur, which may potentially contribute to the “biochar effect” in the rhizosphere. This study is the first to provide empirical evidence that biochar amendment can alter the soil bacterial community assimilating plant-derived C; this may have consequences for nutrient cycling and improving plant performance in intercropping systems.

Effects of tetracycline residuals on humification, microbial profile and antibiotic resistance genes during vermicomposting of dewatered sludge

Vermicomposting is a green technology used in the recycling of sewage sludge using the joint action of earthworms and microorganisms. Although tetracycline is present in abundance in sewage sludge, little attention has been given to its influence on vermicomposts. This study investigated the effects of different tetracycline concentrations (0, 100, 500 and 1000 mg/kg) on the decomposition of organic matter, microbial community and antibiotic resistance genes (ARGs) during vermicomposting of spiked sludge. The results showed that 100 mg/kg tetracycline could stimulate earthworms’ growth, accompanied by the highest humification and decomposition rates of organic matter in the sludge. The abundance of active microbial cells and diversity decreased with the increase in tetracycline concentrations. The member of Bacteroidetes dominated in the tetracycline spiked treatments, especially in the higher concentration treatments. Compared to its counterparts, the addition of tetracycline significantly increased the abundances of ARGs (tetC, tetM, tetX, tetG and tetW) and Class 1 integron (int-1) by 4.7–186.9 folds and 4.25 folds, respectively. The genera of Bacillus and Mycobacterium were the possible bacterial pathogen hosts of ARGs enriched in tetracycline added group. This study suggests that higher concentration of tetracycline residual can modify microbial communities and increase the dissemination risk of ARGs for final sludge vermicompost.

Enrichment and characterization of an environmental microbial consortium displaying efficient keratinolytic activity

Keratin refers to a group of insoluble and recalcitrant protein materials. Slaughterhouses produce large amount of keratinous byproducts, which are either disposed or poorly valorized through costly thermochemical processes for animal feed formulation. Learning from nature, keratinolytic microbial consortia stand as a cost-efficient and environmental friendly way to valorize this recalcitrant resource. Directed selection was applied to enrich soil-born microbial consortia, using sequential batch cultivations in keratin medium, while measuring enzymes activity and monitoring consortia compositions via 16S rRNA gene amplicon sequencing. A promising microbial consortium KMCG6, featuring mainly members of Bacteroidetes and Proteobacteria, was obtained. It possessed keratinolytic activity with <25% residual substrate remaining, which also displayed a high degradation reproducibility level after long-term cryopreservation. This work represents an advance in the field of α-keratin degradation with potential for practical applications.

Taxonomic profiles in metagenomic analyses of free-living microbial communities in the Ofunato Bay

The Ofunato Bay in Iwate Prefecture, Japan is a deep coastal bay located at the center of the Sanriku Rias Coast and considered an economically and environmentally important asset. Here, we describe the first whole genome sequencing (WGS) study on the microbial community of the bay, where surface water samples were collected from three stations along its length to cover the entire bay; we preliminarily sequenced a 0.2 μm filter fraction among sequentially size-fractionated samples of 20.0, 5.0, 0.8 and 0.2 μm filters, targeting the free-living fraction only. From the 0.27–0.34 Gb WGS library, 0.9 × 106–1.2 × 106 reads from three sampling stations revealed 29 bacterial phyla (~80% of assigned reads), 3 archaeal phyla (~4%) and 59 eukaryotic phyla (~15%). Microbial diversity obtained from the WGS approach was compared with 16S rRNA gene results by mining WGS metagenomes, and we found similar estimates. The most frequently recovered bacterial sequences were Proteobacteria, predominantly comprised of 18.0–19.6% Planktomarina (Family Rhodobacteraceae) and 13.7–17.5% Candidatus Pelagibacter (Family Pelagibacterales). Other dominant bacterial genera, including Polaribacter (3.5–6.1%), Flavobacterium (1.8–2.6%), Sphingobacterium (1.4–1.6%) and Cellulophaga (1.4–2.0%), were members of Bacteroidetes and likely associated with the degradation and turnover of organic matter. The Marine Group I Archaea Nitrosopumilus was also detected. Remarkably, eukaryotic green alga Bathycoccus, Ostreococcus and Micromonas accounted for 8.8–15.2%, 3.6–4.9% and 2.1–3.1% of total read counts, respectively, highlighting their potential roles in the phytoplankton bloom after winter mixing.

Bacterial Preferences for Specific Soil Particle Size Fractions Revealed by Community Analyses.

Genetic fingerprinting demonstrated in previous studies that differently sized soil particle fractions (PSFs; clay, silt, and sand with particulate organic matter (POM)) harbor microbial communities that differ in structure, functional potentials and sensitivity to environmental conditions. To elucidate whether specific bacterial or archaeal taxa exhibit preference for specific PSFs, we examined the diversity of PCR-amplified 16S rRNA genes by high-throughput sequencing using total DNA extracted from three long-term fertilization variants (unfertilized, fertilized with minerals, and fertilized with animal manure) of an agricultural loamy sand soil and their PSFs. The PSFs were obtained by gentle ultrasonic dispersion, wet sieving, and centrifugation. The abundance of bacterial taxa assigned to operational taxonomic units (OTUs) differed less than 2.7% between unfractionated soil and soil based on combined PSFs. Across the three soil variants, no archaeal OTUs, but many bacterial OTUs, the latter representing 34–56% of all amplicon sequences, showed significant preferences for specific PSFs. The sand-sized fraction with POM was the preferred site for members of Bacteroidetes and Alphaproteobacteria, while Gemmatimonadales preferred coarse silt, Actinobacteria and Nitrosospira fine silt, and Planctomycetales clay. Firmicutes were depleted in the sand-sized fraction. In contrast, archaea, which represented 0.8% of all 16S rRNA gene sequences, showed only little preference for specific PSFs. We conclude that differently sized soil particles represent distinct microenvironments that support specific bacterial taxa and that these preferences could strongly contribute to the spatial heterogeneity and bacterial diversity found in soils.

Metagenomic analysis of bacterial community structure and diversity of lignocellulolytic bacteria in Vietnamese native goat rumen.

ObjectiveIn a previous study, analysis of Illumina sequenced metagenomic DNA data of bacteria in Vietnamese goats’ rumen showed a high diversity of putative lignocellulolytic genes. In this study, taxonomy speculation of microbial community and lignocellulolytic bacteria population in the rumen was conducted to elucidate a role of bacterial structure for effective degradation of plant materials.MethodsThe metagenomic data had been subjected into Basic Local Alignment Search Tool (BLASTX) algorithm and the National Center for Biotechnology Information non-redundant sequence database. Here the BLASTX hits were further processed by the Metagenome Analyzer program to statistically analyze the abundance of taxa.ResultsMicrobial community in the rumen is defined by dominance of Bacteroidetes compared to Firmicutes. The ratio of Firmicutes versus Bacteroidetes was 0.36:1. An abundance of Synergistetes was uniquely identified in the goat microbiome may be formed by host genotype. With regard to bacterial lignocellulose degraders, the ratio of lignocellulolytic genes affiliated with Firmicutes compared to the genes linked to Bacteroidetes was 0.11:1, in which the genes encoding putative hemicellulases, carbohydrate esterases, polysaccharide lyases originated from Bacteroidetes were 14 to 20 times higher than from Firmicutes. Firmicutes seem to possess more cellulose hydrolysis capacity showing a Firmicutes/Bacteroidetes ratio of 0.35:1. Analysis of lignocellulolytic potential degraders shows that four species belonged to Bacteroidetes phylum, while two species belonged to Firmicutes phylum harbouring at least 12 different catalytic domains for all lignocellulose pretreatment, cellulose, as well as hemicellulose saccharification.ConclusionBased on these findings, we speculate that increasing the members of Bacteroidetes to keep a low ratio of Firmicutes versus Bacteroidetes in goat rumen has resulted most likely in an increased lignocellulose digestion.

Comparative Metagenomics of the Polymicrobial Black Band Disease of Corals.

Black Band Disease (BBD), the destructive microbial consortium dominated by the cyanobacterium Roseofilum reptotaenium, affects corals worldwide. While the taxonomic composition of BBD consortia has been well-characterized, substantially less is known about its functional repertoire. We sequenced the metagenomes of Caribbean and Pacific black band mats and cultured Roseofilum and obtained five metagenome-assembled genomes (MAGs) of Roseofilum, nine of Proteobacteria, and 12 of Bacteroidetes. Genomic content analysis suggests that Roseofilum is a source of organic carbon and nitrogen, as well as natural products that may influence interactions between microbes. Proteobacteria and Bacteroidetes members of the disease consortium are suited to the degradation of amino acids, proteins, and carbohydrates. The accumulation of sulfide underneath the black band mat, in part due to a lack of sulfur oxidizers, contributes to the lethality of the disease. The presence of sulfide:quinone oxidoreductase genes in all five Roseofilum MAGs and in the MAGs of several heterotrophs demonstrates that resistance to sulfide is an important characteristic for members of the BBD consortium.

An alternative polysaccharide uptake mechanism of marine bacteria

Heterotrophic microbial communities process much of the carbon fixed by phytoplankton in the ocean, thus having a critical role in the global carbon cycle. A major fraction of the phytoplankton-derived substrates are high-molecular-weight (HMW) polysaccharides. For bacterial uptake, these substrates must initially be hydrolysed to smaller sizes by extracellular enzymes. We investigated polysaccharide hydrolysis by microbial communities during a transect of the Atlantic Ocean, and serendipitously discovered—using super-resolution structured illumination microscopy—that up to 26% of total cells showed uptake of fluorescently labelled polysaccharides (FLA-PS). Fluorescence in situ hybridisation identified these organisms as members of the bacterial phyla Bacteroidetes and Planctomycetes and the gammaproteobacterial genus Catenovulum. Simultaneous membrane staining with nile red indicated that the FLA-PS labelling occurred in the cell but not in the cytoplasm. The dynamics of FLA-PS staining was further investigated in pure culture experiments using Gramella forsetii, a marine member of Bacteroidetes. The staining patterns observed in environmental samples and pure culture tests are consistent with a ‘selfish’ uptake mechanisms of larger oligosaccharides (>600 Da), as demonstrated for gut Bacteroidetes. Ecologically, this alternative polysaccharide uptake mechanism secures substantial quantities of substrate in the periplasmic space, where further processing can occur without diffusive loss. Such a mechanism challenges the paradigm that hydrolysis of HMW substrates inevitably yields low-molecular-weight fragments that are available to the surrounding community and demonstrates the importance of an alternative mechanism of polysaccharide uptake in marine bacteria.

Identification of 2-keto-3-deoxy-d-Gluconate Kinase and 2-keto-3-deoxy-d-Phosphogluconate Aldolase in an Alginate-Assimilating Bacterium, Flavobacterium sp. Strain UMI-01.

Recently, we identified an alginate-assimilating gene cluster in the genome of Flavobacterium sp. strain UMI-01, a member of Bacteroidetes. Alginate lyase genes and a 4-deoxy-l-erythro-5-hexoseulose uronic acid (DEH) reductase gene in the cluster have already been characterized; however, 2-keto-3-deoxy-d-gluconate (KDG) kinase and 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase genes, i.e., flkin and flald, still remained uncharacterized. The amino acid sequences deduced from flkin and flald showed low identities with those of corresponding enzymes of Saccharophagus degradans 2-40T, a member of Proteobacteria (Kim et al., Process Biochem., 2016). This led us to consider that the DEH-assimilating enzymes of Bacteroidetes species are somewhat deviated from those of Proteobacteria species. Thus, in the present study, we first assessed the characteristics in the primary structures of KDG kinase and KDG aldolase of the strain UMI-01, and then investigated the enzymatic properties of recombinant enzymes, recFlKin and recFlAld, expressed by an Escherichia coli expression system. Multiple-sequence alignment among KDG kinases and KDG aldolases from several Proteobacteria and Bacteroidetes species indicated that the strain UMI-01 enzymes showed considerably low sequence identities (15%–25%) with the Proteobacteria enzymes, while they showed relatively high identities (47%–68%) with the Bacteroidetes enzymes. Phylogenetic analyses for these enzymes indicated the distant relationship between the Proteobacteria enzymes and the Bacteroidetes enzymes, i.e., they formed distinct clusters in the phylogenetic tree. recFlKin and recFlAld produced with the genes flkin and flald, respectively, were confirmed to show KDG kinase and KDPG aldolase activities. Namely, recFlKin produced 1.7 mM KDPG in a reaction mixture containing 2.5 mM KDG and 2.5 mM ATP in a 90-min reaction, while recFlAld produced 1.2 mM pyruvate in the reaction mixture containing 5 mM KDPG at the equilibrium state. An in vitro alginate-metabolizing system constructed from recFlKin, recFlAld, and previously reported alginate lyases and DEH reductase of the strain UMI-01 could convert alginate to pyruvate and glyceraldehyde-3-phosphate with an efficiency of 38%.

Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments.

Alginates are abundant polysaccharides in brown algae that constitute an important energy source for marine heterotrophic bacteria. Despite the key role of alginate degradation processes in the marine carbon cycle, little information is available on the bacterial populations involved in these processes. The aim of this work was to gain a better understanding of alginate utilization capabilities in cold coastal environments. Sediment metagenomes from four high-latitude regions of both Hemispheres were interrogated for alginate lyase gene homologue sequences and their genomic context. Sediments contained highly abundant and diverse bacterial assemblages with alginolytic potential, including members of Bacteroidetes and Proteobacteria, as well as several poorly characterized taxa. The microbial communities in Arctic and Antarctic sediments exhibited the most similar alginolytic profiles, whereas brackish sediments showed distinct structures with a higher proportion of novel genes. Examination of the gene neighbourhood of the alginate lyase homologues revealed distinct patterns depending on the potential lineage of the scaffolds, with evidence of evolutionary relationships among alginolytic gene clusters from Bacteroidetes and Proteobacteria. This information is relevant for understanding carbon fluxes in cold coastal environments and provides valuable information for the development of biotechnological applications from brown algae biomass.

Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies

BackgroundThe diverse microbial communities in agricultural biogas fermenters are assumed to be well adapted for the anaerobic transformation of plant biomass to methane. Compared to natural systems, biogas reactors are limited in their hydrolytic potential. The reasons for this are not understood.ResultsIn this paper, we show that a typical industrial biogas reactor fed with maize silage, cow manure, and chicken manure has relatively lower hydrolysis rates compared to feces samples from herbivores. We provide evidence that on average, 2.5 genes encoding cellulolytic GHs/Mbp were identified in the biogas fermenter compared to 3.8 in the elephant feces and 3.2 in the cow rumen data sets. The ratio of genes coding for cellulolytic GH enzymes affiliated with the Firmicutes versus the Bacteroidetes was 2.8:1 in the biogas fermenter compared to 1:1 in the elephant feces and 1.4:1 in the cow rumen sample. Furthermore, RNA-Seq data indicated that highly transcribed cellulases in the biogas fermenter were four times more often affiliated with the Firmicutes compared to the Bacteroidetes, while an equal distribution of these enzymes was observed in the elephant feces sample.ConclusionsOur data indicate that a relatively lower abundance of bacteria affiliated with the phylum of Bacteroidetes and, to some extent, Fibrobacteres is associated with a decreased richness of predicted lignocellulolytic enzymes in biogas fermenters. This difference can be attributed to a partial lack of genes coding for cellulolytic GH enzymes derived from bacteria which are affiliated with the Fibrobacteres and, especially, the Bacteroidetes. The partial deficiency of these genes implies a potentially important limitation in the biogas fermenter with regard to the initial hydrolysis of biomass. Based on these findings, we speculate that increasing the members of Bacteroidetes and Fibrobacteres in biogas fermenters will most likely result in an increased hydrolytic performance.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-016-0534-x) contains supplementary material, which is available to authorized users.

Community dynamics and the lower airway microbiota in stable chronic obstructive pulmonary disease, smokers and healthy non-smokers

RationaleThe role bacteria play in the progression of COPD has increasingly been highlighted in recent years. However, the microbial community complexity in the lower airways of patients with COPD is...