Members Of Firmicutes Research Articles

Putative Nitrogen-Fixing Bacteria Associated With the Rhizosphere and Root Endosphere of Wheat Plants Grown in an Andisol From Southern Chile.

Acidic ash derived volcanic soils (Andisols) support 50% of cereal production in Chile. Nitrogen (N) is essential for cereal crops and commonly added as urea with consequent environmental concerns due to leaching. Despite the relevance of N to plant growth, few studies have focused on understanding the application, management and ecological role of N2-fixing bacterial populations as tool for improve the N nutrition of cereal crops in Chile. It is known that N2-fixing bacteria commonly inhabits diverse plant compartments (e.g., rhizosphere and root endosphere) where they can supply N for plant growth. Here, we used culture-independent and dependent approaches to characterize and compare the putative N2-fixing bacteria associated with the rhizosphere and root endosphere of wheat plants grown in an Andisol from southern Chile. Our results showed significantly greater bacterial loads in the rhizosphere than the root endosphere. Quantitative PCR results indicated that the copy number of the 16S rRNA gene ranged from 1012~1013 and 107~108 g−1 sample in rhizosphere and root endosphere, respectively. The nifH gene copy number ranged from 105~106 and 105 g−1 sample in rhizosphere and root endosphere, respectively. The total culturable bacteria number ranged from 109~1010 and 107~108 CFU g−1 sample in rhizosphere and 104~105 and 104 CFU g−1 sample in root endosphere using LB and NM-1 media, respectively. Indirect counts of putative N2-fixing bacteria were 103 and 102~103 CFU g−1 sample in rhizosphere and root endosphere using NFb medium, respectively. Sequencing of 16S rRNA genes from randomly selected putative N2-fixing bacteria revealed the presence of members of Proteobacteria (Bosea and Roseomonas), Actinobacteria (Georgenia, Mycobacterium, Microbacterium, Leifsonia, and Arthrobacter), Bacteroidetes (Chitinophaga) and Firmicutes (Bacillus and Psychrobacillus) taxa. Differences in 16S rRNA and putative nifH-containing bacterial communities between rhizosphere and root endosphere were shown by denaturing gradient gel electrophoresis (DGGE). This study shows a compartmentalization between rhizosphere and root endosphere for both the abundance and diversity of total (16S rRNA) and putative N2-fixing bacterial communities on wheat plants grown in Chilean Andisols. This information can be relevant for the design and application of agronomic strategies to enhance sustainable N-utilization in cereal crops in Chile.

Linking bacterial and eukaryotic microbiota to litter chemistry: Combining next generation sequencing with 13C CPMAS NMR spectroscopy

Microbial succession over decomposing litter is controlled by biotic interactions, dispersal limitation, grazing pressure, and substrate chemical changes. Recent evidence suggests that the changes in litter chemistry and microbiome during decomposition are interdependent. However, most previous studies separately addressed the microbial successional dynamics or the molecular changes of decomposing litter. Here, we combined litter chemical characterization by 13C NMR spectroscopy with next generation sequencing to compare leaf litter chemistry and microbiome dynamics using 30 litter types, either fresh or decomposed for 30 and 180 days.We observed a decrease of cellulose and C/N ratio during decomposition, while lignin content and lignin/N ratio showed the opposite pattern. 13C NMR revealed significant chemical changes as microbial decomposition was proceeding, with a decrease in O-alkyl C and an increase in alkyl C and methoxyl C relative abundances. Overall, bacterial and eukaryotic taxonomical richness increased with litter age. Among Bacteria, Proteobacteria dominated all undecomposed litters but this group was progressively replaced by members of Actinobacteria, Bacteroidetes, and Firmicutes. Nitrogen-fixing genera such as Beijerinckia and Rhizobium occurred both in undecomposed as well as in aged litters. Among Eukarya, fungi belonging to the Ascomycota phylum were dominant in undecomposed litter with the typical phyllospheric genus Aureobasidium. In aged litters, phyllospheric species were replaced by zygomycetes and other ascomycetous and basidiomycetous fungi. Our analysis of decomposing litter highlighted an unprecedented, widespread occurrence of protists belonging to the Amebozoa and Cercozoa. Correlation network analysis showed that microbial communities are non-randomly structured, showing strikingly distinct composition in relation to litter chemistry. Our data demonstrate that the importance of litter chemistry in shaping microbial community structure increased during the decomposition process, being of little importance for freshly fallen leaves.

Alterations in gut bacterial and fungal microbiomes are associated with bacterial Keratitis, an inflammatory disease of the human eye

Dysbiosis, or imbalance in the gut microbiome, has been implicated in auto-immune, inflammatory, neurological diseases as well as in cancers. More recently it has also been shown to be associated with ocular diseases. In the present study, the association of gut microbiome dysbiosis with bacterial Keratitis, an inflammatory eye disease which significantly contributes to corneal blindness, was investigated. Bacterial and fungal gut microbiomes were analysed using fecal samples of healthy controls (HC, n = 21) and bacterial Keratitis patients (BK, n = 19). An increase in abundance of several antiinflammatory organisms including Dialister, Megasphaera, Faecalibacterium, Lachnospira, Ruminococcus and Mitsuokella and members of Firmicutes, Veillonellaceae, Ruminococcaceae and Lachnospiraceae was observed in HC compared to BK patients in the bacterial microbiome. In the fungal microbiome, a decrease in the abundance of Mortierella, Rhizopus, Kluyveromyces, Embellisia and Haematonectria and an increase in the abundance of pathogenic fungi Aspergillus and Malassezia were observed in BK patients compared to HC. In addition, heatmaps, PCoA plots and inferred functional profiles also indicated significant variations between the HC and BK microbiomes, which strongly suggest dysbiosis in the gut microbiome of BK patients. This is the first study demonstrating the association of gut microbiome with the pathophysiology of BK and thus supports the gut-eye axis hypothesis. Considering that Keratitis affects about 1 million people annually across the globe, the data could be the basis for developing alternate strategies for treatment like use of probiotics or fecal transplantation to restore the healthy microbiome as a treatment protocol for Keratitis.

Iopamidol degradation with ZVI- and ZVA-activated chemical oxidation: Investigation of toxicity, anaerobic inhibition and microbial communities

Treatment of aqueous iopamidol (IOPA, 2 mg/L), an iodinated organic X-ray contrast chemical and micropollutant, with nano-sized zero-valent iron (ZVI) and aluminum (ZVA)-activated hydrogen peroxide (HP) and persulfate (PS) oxidation processes was investigated. Changes in acute toxicity, anaerobic digestion, biogas yield and microbial community were further examined to question the ecotoxicological safety and bioamenability of the proposed treatment systems. For this purpose, two different bioassays were conducted with V. fischeri and P. subcapitata. The cumulative biogas production was monitored in batch anaerobic digestion tests. The microbial community was identified by Illumina MiSeq next generation sequencing (NGS) technology and abundant bacteria and archaea were analysed in the biomass samples taken from anaerobic reactors. The application of activated HP (1.00 mM) and PS (0.50 mM) treatments under acidic conditions (pH 3) resulted in complete IOPA removal. The original IOPA sample caused 5% and 74% inhibitions to V. fischeri and P. subcapitata, respectively. The relative inhibition towards P. subcapitata increased from 74% to 97% and 93% after 5 min HP/ZVI and 120 min PS/ZVA treatments, respectively. No meaningful changes in terms of digestion performance and cumulative biogas production in the presence of untreated and HP/ZVI- or PS/ZVA-treated IOPA samples were evidenced. Moreover, all biomass samples were populated by a bacterial consortium related to different members of Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Hydrogenotrophic (Methanospirillum, Methanobacterium) and acetoclastic (Methanosaeta, Methanosarcina) methanogens were the prevalent members of archaea at genus level. An increase in relative abundance was only identified in Methanobacterium under the phylum namely Euryarchaeota.

PLGA-encapsulated CpG ODN and Campylobacter jejuni lysate modulate cecal microbiota composition in broiler chickens experimentally challenged with C. jejuni

Campylobacter jejuni is a leading bacterial cause of human gastroenteritis. Reducing Campylobacter numbers in the intestinal tract of chickens will minimize transmission to humans, thereby reducing the incidence of infection. We have previously shown that oral pre-treatment of chickens with C. jejuni lysate and Poly D, L-lactide-co-glycolide polymer nanoparticles (PLGA NPs) containing CpG oligodeoxynucleotide (ODN) can reduce the number of C. jejuni in infected chickens. In the current study, the effects of these pre-treatments on the composition and functional diversity of the cecal microbiota, in chickens experimentally infected with C. jejuni, were investigated using next-generation sequencing. The taxonomic composition analysis revealed a reduction in cecal microbial diversity and considerable changes in the taxonomic profiles of the microbial communities of C. jejuni-challenged chickens. On the other hand, irrespective of the dose, the microbiota of PLGA-encapsulated CpG ODN- and C. jejuni lysate-treated chickens exhibited higher microbial diversity associated with high abundance of members of Firmicutes and Bacteroidetes and lower numbers of Campylobacter than untreated-chickens. These findings suggest that oral administration of encapsulated CpG ODN and C. jejuni lysate can reduce colonization by C. jejuni by enhancing the proliferation of specific microbial groups. The mechanisms that mediate these changes remain, however, to be elucidated.

Ultraviolet Irradiation of Skin Alters the Faecal Microbiome Independently of Vitamin D in Mice.

Reduced sunlight exposure has been associated with an increased incidence of Crohn’s disease and ulcerative colitis. The effect of ultraviolet radiation (UVR) on the faecal microbiome and susceptibility to colitis has not been explored. C57Bl/6 female mice were fed three different vitamin D-containing diets for 24 days before half of the mice in each group were UV-irradiated (1 kJ/m2) for each of four days, followed by twice-weekly irradiation of shaved dorsal skin for 35 days. Faecal DNA was extracted and high-throughput sequencing of the 16S RNA gene performed. UV irradiation of skin was associated with a significant change in the beta-diversity of faeces compared to nonirradiated mice, independently of vitamin D. Specifically, members of phylum Firmicutes, including Coprococcus, were enriched, whereas members of phylum Bacteroidetes, such as Bacteroidales, were depleted. Expression of colonic CYP27B1 increased by four-fold and IL1β decreased by five-fold, suggesting a UVR-induced anti-inflammatory effect. UV-irradiated mice, however, were not protected against colitis induced by dextran sodium sulfate (DSS), although distinct faecal microbiome differences were documented post-DSS between UV-irradiated and nonirradiated mice. Thus, skin exposure to UVR alters the faecal microbiome, and further investigations to explore the implications of this in health and disease are warranted.

Association Between Intestinal Microbiota Collected at Hospital Admission and Outcomes of Patients With Cirrhosis

Inpatients with cirrhosis are prone to develop acute-on-chronic liver failure (ACLF). ACLF is associated with dysbiosis of the intestinal microbiota, which might serve as a prognostic factor. We investigated whether features of the intestinal microbiota associate organ failure, transfer to intensive care, and mortality within 30 days in patients admitted to the hospital with cirrhosis. Stool samples were collected from 181 patients with cirrhosis (age 56 years; mean model for end-stage liver disease score, 21; 43% with infections) at time of admission, from multiple hospitals in North America. Patients were followed for 30 days for development of ACLF, extra-hepatic organ failures, and death or hospice care. Microbiota were analyzed by 16s rRNA sequencing for alpha diversity (within groups), beta diversity (between groups), cirrhosis dysbiosis ratio (CDR), and taxa that differed between groups with vs without negative outcomes (individual organ failures, transfer to intensive care, ACLF, death, or hospice). Regression analyses were performed using microbial and clinical variables for each outcome. ACLF developed in 8% of study subjects; 16% were transferred to intensive care and 21% died. Beta diversity of the intestinal microbiome was significantly different, whereas alpha diversity was similar, between subjects with vs without outcomes. The CDR was lower in subjects who developed ACLF, especially among those with renal failure. Taxa belonging to phylum Proteobacteria (Enterobacteriaceae, Campylobacteriaceae, and Pasteurellaceae) and Firmicutes (Enterococcaceae and Streptococcaceae) were associated with development of negative outcomes, whereas other Firmicutes members (Lachnospiraceae and Clostridiales) reduced risk of negative outcomes. Changes in the microbiota associated with extra-hepatic organ failure, transfer to intensive care, ACLF, and death, independently on logistic regression analyses. In hospitalized patients with cirrhosis, dysbiosis of the intestinal microbiota on admission (particularly changes in Protebacteria constituents) associates with increased risk of extra-hepatic organ failure, ACLF, and death, independent of clinical factors. Strategies to reduce gut dysbiosis might improve outcomes of patients with cirrhosis.

Lignolytic-consortium omics analyses reveal novel genomes and pathways involved in lignin modification and valorization

BackgroundLignin is a heterogeneous polymer representing a renewable source of aromatic and phenolic bio-derived products for the chemical industry. However, the inherent structural complexity and recalcitrance of lignin makes its conversion into valuable chemicals a challenge. Natural microbial communities produce biocatalysts derived from a large number of microorganisms, including those considered unculturable, which operate synergistically to perform a variety of bioconversion processes. Thus, metagenomic approaches are a powerful tool to reveal novel optimized metabolic pathways for lignin conversion and valorization.ResultsThe lignin-degrading consortium (LigMet) was obtained from a sugarcane plantation soil sample. The LigMet taxonomical analyses (based on 16S rRNA) indicated prevalence of Proteobacteria, Actinobacteria and Firmicutes members, including the Alcaligenaceae and Micrococcaceae families, which were enriched in the LigMet compared to sugarcane soil. Analysis of global DNA sequencing revealed around 240,000 gene models, and 65 draft bacterial genomes were predicted. Along with depicting several peroxidases, dye-decolorizing peroxidases, laccases, carbohydrate esterases, and lignocellulosic auxiliary (redox) activities, the major pathways related to aromatic degradation were identified, including benzoate (or methylbenzoate) degradation to catechol (or methylcatechol), catechol ortho-cleavage, catechol meta-cleavage, and phthalate degradation. A novel Paenarthrobacter strain harboring eight gene clusters related to aromatic degradation was isolated from LigMet and was able to grow on lignin as major carbon source. Furthermore, a recombinant pathway for vanillin production was designed based on novel gene sequences coding for a feruloyl-CoA synthetase and an enoyl-CoA hydratase/aldolase retrieved from the metagenomic data set.ConclusionThe enrichment protocol described in the present study was successful for a microbial consortium establishment towards the lignin and aromatic metabolism, providing pathways and enzyme sets for synthetic biology engineering approaches. This work represents a pioneering study on lignin conversion and valorization strategies based on metagenomics, revealing several novel lignin conversion enzymes, aromatic-degrading bacterial genomes, and a novel bacterial strain of potential biotechnological interest. The validation of a biosynthetic route for vanillin synthesis confirmed the applicability of the targeted metagenome discovery approach for lignin valorization strategies.

Assessment of indoor air environment of a Nigerian museum library and its biodeteriorated books using culture-dependent and –independent techniques

The surface-associated microflora on four deteriorated historical books kept in the library of a Nigerian museum were studied to identify microbial communities present, determine potential biodeteriogens and evaluate microbial aeroflora as a putative source of contamination. The application of culture-independent and -dependent techniques identified members of Actinobacteria, Bacteriodetes, Firmicutes and Proteobacteria as bacterial colonizers of the volumes, with Bacillus, Stenotrophomonas and Variovorax as the dominant genera. The fungal community belonged to Ascomycota with Aspergillus and Penicillium as the prevalent taxa. The retrieved microorganisms included some species that had never been detected on documentary heritage, though they have been found in association with soil particles and insects. Cellulolytic screening assay ascertained thirteen bacterial and six fungal isolates as potential biodeteriogens of the said documents. The higher microbial build-up on the discoloured areas compared to the control areas of the books highlighted microorganisms as a cause of the deterioration. The airborne microbial population, determined with passive sampling, revealed the microbial cell density to be higher in the rainy season than the dry. This is the first report on the use of both genetic fingerprinting and traditional methods in a biodeterioration study of books in Nigeria. The findings of the study should be taken into account to ensure the proper preservation of written heritage.

Cake layer bacterial communities during different biofouling stages in full-scale membrane bioreactors

A detailed understanding of the bacterial communities in the cake layers formed on the membrane surface is required to control biofouling in a membrane bioreactor (MBR). This study aimed to investigate the dynamics of the cake layer bacterial communities in full-scale MBRs operated in a wastewater treatment plant in Japan and to identify the key bacteria responsible for cake layer formation. The bacterial communities in the cake layer and the activated sludge were analyzed using 16S rRNA gene amplicon sequencing when biofouling occurred under different fouling conditions. The most dominant phyla in activated sludge were almost always Proteobacteria and Bacteroidetes. By contrast, when the cake layer had unique bacterial communities distinguishable from those in the activated sludge, members of Firmicutes were highly dominant in the cake layer, irrespective of the fouling conditions. This study reported for the first time that Firmicutes play an important role throughout the biofouling process.

Impact of copper on the diazotroph abundance and community composition during swine manure composting

Biological nitrogen fixation is a major pathway in ecosystems. This study investigated the effects of adding Cu at different levels (0, 200, and 2000 mg kg−1) on the diazotroph community during swine manure composting. Quantitative PCR and high-throughput sequencing were used to analyze the abundances of diazotrophs and the community composition based on the nifH gene. The nifH gene copy number was relatively high in the early stage of composting and Cu had a significant inhibitory effect on the nifH copy number. Furthermore, Cu decreased the diversity of nifH and changed the microbial community structure in the early stage. The nifH genes from members of Firmicutes and Clostridium were most abundant. Co-occurrence ecological network analysis showed that the Cu treatments affected the co-occurrence patterns of diazotroph communities and reduced the associations between different diazotrophs. Interestingly, Cu may weaken symbiotic diazotrophic interactions and enhance the roles of free-living diazotrophs.

Microbial Flora Associated with the Halophyte-Salsola imbricate and Its Biotechnical Potential.

Halophytes are associated with the intertidal forest ecosystem of Saudi Arabia and seemingly have an immense potential for yielding useful and important natural products. In this study we have aimed to isolate and characterize the endophytic and rhizospheric bacterial communities from the halophyte, Salsola imbricata, In addition these bacterial strains were identified and selected strains were further studied for bioactive secondary metabolites. At least 168 rhizspheric and endophytic bacteria were isolated and of these 22 were active antagonists against the oomycetous fungal plant pathogens, Phytophthora capsici and Pythium ultimum. Active cultures were mainly identified with molecular techniques (16S r DNA) and this revealed 95.7–100% sequence similarities with relevant type strains. These microorgansims were grouped into four major classes: Actinobacteria, Firmicutes, β-Proteobacteria, and γ-Proteobacteria. Production of fungal cell wall lytic enzymes was detected mostly in members of Actinobacteria and Firmicutes. PCR screening for type I polyketide synthases (PKS-I), type II polyketide synthases (PKS-II) and nonribosomal peptide synthetases (NRPS) revealed 13 of the 22 strains (59%) were positive for at least one of these important biosynthetic genes that are known to be involved in the synthesis of important antibiotics. Four bacterial strains of Actinobacteria with potential antagonistic activity including two rhizobacteria, EA52 (Nocardiopsis sp.), EA58 (Pseudonocardia sp.) and two endophytic bacteria Streptomyces sp. (EA65) and Streptomyces sp. (EA67) were selected for secondary metabolite analyses using LC-MS. As a result, the presence of different bioactive compounds in the culture extracts was detected some of which are already reported for their diverse biological activities including antibiotics such as Sulfamethoxypyridazine, Sulfamerazine, and Dimetridazole. In conclusion, this study provides an insight into antagonistic bacterial population especially the Actinobacteria from S. imbricata, producing antifungal metabolites of medical significance and characterized taxonomically in future.

Breast abscess caused by Staphylococcus aureus in 2 adolescent girls with atopic dermatitis

Atopic dermatitis (AD) is a chronic inflammatory skin disease in children. Patients with AD experience a high rate of colonization of the skin surface by Staphylococcus aureus. Because of a skin barrier defect, there is a potential risk of staphylococcal invasive infection in patients with AD. Here, we present 2 cases of breast abscess caused by S. aureus in 2 adolescent girls with severe AD. Methicillin-sensitive S. aureus was identified from the breast abscess material. They were treated with appropriate antibiotics, however surgical drainage of the abscess was needed in case 1. Identical strains were found from the breast abscess material as well as the lesional and the nonlesional skin of the patients through matrixassisted laser desorption/ionization time-of-flight analysis. We characterized the differential abundance of Firmicutes phylum in patients' skin in microbiota analysis. In particular, S. aureus, a member of Firmicutes, differed significantly between the lesional and the normal-appearing skin. Our cases demonstrate the potential severity of bacterial deep tissue infection in AD and the dysbiosis of skin microbiota may be involved in inflammation in AD.

Investigating monsoon and post-monsoon variabilities of bacterioplankton communities in a mangrove ecosystem.

In mangrove environments, bacterioplankton communities constitute an important component of aquatic biota and play a major role in ecosystem processes. Variability of bacterioplankton communities from Sundarbans mangrove, located in the Indian subcontinent in South Asia and sits on the apex of Bay of Bengal, was investigated over monsoon and post-monsoon seasons. The study was undertaken in two stations in Sundarbans using 16S rRNA clone library and Illumina MiSeq approaches with focus on the functionally important members that participate in coastal biogeochemical cycling. Out of 544 sequenced clones, Proteobacteria dominated the study area (373 sequences) with persistence of two major classes, namely, Gammaproteobacteria and Alphaproteobacteria across both monsoon and post-monsoon seasons in both stations. Several sequences belonging to Sphingomonadales, Chromatiales, Alteromonadales, Oceanospirillales, and Bacteroidetes were encountered that are known to play important roles in coastal carbon cycling. Some sequences showed identity with published uncultured Planctomycetes and Chloroflexi highlighting their role in nitrogen cycling. The detection of two novel clades highlighted the existence of indigenous group of bacterioplankton that may play important roles in this ecosystem. The eubacterial V3-V4 region from environmental DNA extracted from the above two stations, followed by sequencing in Illumina MiSeq system, was also targeted in the study. A congruency between the clone library and Illumina approaches was observed. Strong variability in bacterioplankton community structure was encountered at a seasonal scale in link with precipitation. Drastic increase in sediment associated bacteria such as members of Firmicutes and Desulfovibrio was found in monsoon hinting possible resuspension of sediment-dwelling bacteria into the overlying water column. Principal component analysis (PCA) revealed dissolved ammonium and dissolved nitrate to account for maximum variation observed in the bacterioplankton community structure. Overall, the study showed that a strong interplay exists between environmental parameters and observed variability in bacterioplankton communities as a result of precipitation which can ultimately influence processes and rates linked to coastal biogeochemical cycles.

Inducible cellulase production from an organic solvent tolerant Bacillus sp. SV1 and evolutionary divergence of endoglucanase in different species of the genus Bacillus.

Bacteria are important sources of cellulases with various industrial and biotechnological applications. In view of this, a non-hemolytic bacterial strain, tolerant to various environmental pollutants (heavy metals and organic solvents), showing high cellulolytic index (7.89) was isolated from cattle shed soil and identified as Bacillus sp. SV1 (99.27% pairwise similarity with Bacillus korlensis). Extracellular cellulases showed the presence of endoglucanase, total cellulase and β-glucosidase activities. Cellulase production was induced in presence of cellulose (3.3 times CMCase, 2.9 times FPase and 2.1 times β-glucosidase), and enhanced (115.1% CMCase) by low-cost corn steep solids. An in silico investigation of endoglucanase (EC 3.2.1.4) protein sequences of three Bacillus spp. as query, revealed their similarities with members of nine bacterial phyla and to Eukaryota (represented by Arthropoda and Nematoda), and also highlighted of a convergent and divergent evolution from other enzymes of different substrate [(1,3)-linked beta-d-glucans, xylan and chitosan] specificities. Characteristic conserved signature indels were observed among members of Actinobacteria (7 aa insert) and Firmicutes (9 aa insert) that served as a potential tool in support of their relatedness in phylogenetic trees.

Alterations in ruminal bacterial populations at induction and recovery from diet-induced milk fat depression in dairy cows

Ten ruminally cannulated Holstein cows were used in a crossover design that investigated changes in ruminal bacterial populations in response to induction and recovery from diet-induced milk fat depression (MFD). Further, the effect on the ruminal microbiota of the cows with diet-induced milk fat depression inoculated with rumen contents from non-milk fat-depressed donor cows was evaluated. Milk fat depression was induced during the first 10 d of each period by feeding a low-fiber, high-starch, and high-polyunsaturated fatty acid diet (26.1% neutral detergent fiber, 28.1% starch, 5.8% total fatty acids, and 1.9% C18:2), resulting in a 30% decrease in milk fat yield. Induction was followed by a recovery phase, where all cows were switched to a high-fiber, low-starch, and low-polyunsaturated fatty acid diet (31.8% neutral detergent fiber, 23% starch, 4.2% total fatty acids, and 1.2% C18:2) and were allocated to (1) control (no inoculation) or (2) ruminal inoculation with donor cow digesta (8 kg/d for 6 d). Ruminal samples were collected at the end of induction (d 10) and during recovery (d 13, 16, and 28), separated to solid and liquid fractions, extracted for DNA, PCR- amplified for the V1-V2 region of the 16S rRNA gene, and analyzed for bacterial diversity. Results indicated that bacterial communities were different between fractions. In each fraction, differences were significant between the induction (d 10) and recovery (d 13, 16, and 28) periods; however, differences were less apparent with time during the recovery period. The MFD (d 10) was typified by a reduction in the relative sequence abundance of Bacteroidetes and an increase in the relative sequence abundance of Firmicutes and Actinobacteria across both fractions. At the genus level, relative sequence abundance of unclassified Lachnospiraceae, Butyrivibrio, Bulleidia, and Coriobacteriaceae were higher on d 10 and were positively correlated with trans-10,cis-12 CLA and the trans-10 isomer, suggesting their potential role in altered biohydrogenation reactions. A switch to the recovery diet resulted in a sharp increase in the Bacteroidetes lineages and a decrease in Firmicutes members on d 13; however, this shift appears to stabilize by d 28, indicating the restoration process for ruminal bacteria from an altered state is gradual and complex. Inoculation of 10% of rumen contents from non-MFD donor cows to MFD cows revealed this procedure had transient effects on only a few bacterial populations, and such effects disappeared after d 16 following cessation of inoculation. It can be concluded that alterations in milk FA profiles at induction are preceded by microbial alterations in the rumen driven by dietary changes.

Effects of dietary raffinose on growth, non-specific immunity, intestinal morphology and microbiome of juvenile hybrid sturgeon (Acipenser baeri Brandt ♀ × A. schrenckii Brandt ♂)

This study was performed to determine the efficacy of raffinose on the growth, non-specific immunity, intestinal morphology and microbiota of juvenile hybrid sturgeon, (Acipenser baeri Brandt ♀ × A. schrenckii Brandt ♂). Hybrid sturgeons were divided into 2 groups and each group was fed with diets supplemented with or without raffinose for 56 days. Hybrid sturgeon fed diet supplemented with raffinose had significantly higher final body weight (FBW), specific growth rate (SGR), and weight gain ratio (WGR) than fish fed the control diet (P < 0.05). Raffinose in diet had no negative effect on feed intake (FI) and feed conversion ratio (FCR) (P > 0.05). Compared with the control diet, the myeloperoxidase (MPO) and respiratory burst (NBT) activitives were significantly higher in sturgeon fed the raffinose supplemented diet (P < 0.05). The increasing of intestinal villi area and mucosal folds were observed in intestinal tract of sturgeon when they fed the raffinose supplemented diet. Meanwhile, the residual bait of intestinal tract was relatively lower in sturgeon with raffinose treatment. High-throughput sequencing revealed that majority of reads derived from the sturgeon digesta were constituted by members of Proteobacteria, Firmicutes, Fusobacteria and Actinobacteria. Shannon's diversity index existed significant difference among dietary treatments indicating that the overall microbial community was modified to a large extent by dietary raffinose. In conclusion, supplementation of the diet with raffinose is capable of improving hybrid sturgeon growth performances and intestinal morphology, modifying the intestinal microbial composition.

16S rDNA-based bacterial diversity analysis of Arabian Sea sediments: A metagenomic approach

Abstract Marine ecosystems are highly productive as they harbor different marine microorganisms. Analysis of microbial diversity from these ecosystems will help identify new microbes having specificity for unique applications. This study deals with the culture-independent assessment of bacterial community structure and diversity of Arabian Sea sediments based on sequence analysis of 16S rDNA clone library. The sequences classified into seven phyla of bacterial domain including members of phylum Proteobacteria, Bacteriodetes, Actinobacteria, Firmicutes, Chloroflexi, Deferribacter and Acidobacterium. Most sequences were identified as phylum Proteobacteria (62.80%), with a dominance of classes Alphaproteobacteria (58.46%) and Gammaproteobacteria (38.46%). 10.47% of the sequences did not fall into any taxonomic hierarchy suggesting the possibility of unexplored/unidentified ones in marine sediments. This study adds to the limited information about the Viable But Not Culturables (VBNCs) in the sediments of Arabian Sea. Further studies are essential to understand the diversity and function in detail.

Exploring a Possible Link between the Intestinal Microbiota and Feed Efficiency in Pigs.

Feed efficiency (FE) is critical in pig production for both economic and environmental reasons. As the intestinal microbiota plays an important role in energy harvest, it is likely to influence FE. Therefore, our aim was to characterize the intestinal microbiota of pigs ranked as low, medium, and high residual feed intake ([RFI] a metric for FE), where genetic, nutritional, and management effects were minimized, to explore a possible link between the intestinal microbiota and FE. Eighty-one pigs were ranked according to RFI between weaning and day 126 postweaning, and 32 were selected as the extremes in RFI (12 low, 10 medium, and 10 high). Intestinal microbiota diversity, composition, and predicted functionality were assessed by 16S rRNA gene sequencing. Although no differences in microbial diversity were found, some RFI-associated compositional differences were revealed, principally among members of Firmicutes, predominantly in feces at slaughter (albeit mainly for low-abundance taxa). In particular, microbes associated with a leaner and healthier host (e.g., Christensenellaceae, Oscillibacter, and Cellulosilyticum) were enriched in low RFI (more feed-efficient) pigs. Differences were also observed in the ileum of low RFI pigs; most notably, Nocardiaceae (Rhodococcus) were less abundant. Predictive functional analysis suggested improved metabolic capabilities in these animals, especially within the ileal microbiota. Higher ileal isobutyric acid concentrations were also found in low RFI pigs. Overall, the differences observed within the intestinal microbiota of low RFI pigs compared with that of their high RFI counterparts, albeit relatively subtle, suggest a possible link between the intestinal microbiota and FE in pigs.IMPORTANCE This study is one of the first to show that differences in intestinal microbiota composition, albeit subtle, may partly explain improved feed efficiency (FE) in low residual feed intake (RFI) pigs. One of the main findings is that, although microbial diversity did not differ among animals of varying FE, specific intestinal microbes could potentially be linked with porcine FE. However, as the factors impacting FE are still not fully understood, intestinal microbiota composition may not be a major factor determining differences in FE. Nonetheless, this work has provided a potential set of microbial biomarkers for FE in pigs. Although culturability could be a limiting factor and intervention studies are required, these taxa could potentially be targeted in the future to manipulate the intestinal microbiome so as to improve FE in pigs. If successful, this has the potential to reduce both production costs and the environmental impact of pig production.

Biofilm communities survey at the areas of salt crystallization on the walls of a decorated shelter listed at UNESCO World cultural Heritage

The microbial diversity on the walls of the UNESCO World cultural Heritage site Laugerie-Haute east shelter, France, was surveyed in a context of degradation by formation of salt efflorescences. Samples of salt efflorescence and underlying rock were collected in autumn and spring. Sessile microorganisms were studied by cultivation, microscopy, and molecular methods. Concentrations of the order of 103 fungal and 107 bacterial cells per gram of sample were quantified by culturing at both seasons. Higher concentrations (107 to 109 cells per gram) of sessile microorganisms were determined by microscopic counting after DAPI staining with a significant increase in sessile cells in spring. The presence of biofilms was confirmed by electron microscopy with the observation of microorganisms embedded in an abundant matrix in association with rock. Members of Firmicutes, Actinobacteria, and Ascomycota were identified among the cultivable sessile microflora. Bacillus herbersteinensis and Engyodontium album were the only microorganisms to be isolated in both seasons. Sequence analysis of 16S rRNA genes and internal transcribed spacer clone libraries showed dominance of Bacteroidetes, Proteobacteria, and Ascomycota. Bacteroidetes and Actinobacteria were more abundant in autumn, and in spring, respectively. Cyanobacteria were present at both seasons. Bacterial richness increased during spring. Whatever the season, clones affiliated to the 4 bacterial genera Aureimonas, Sphingopyxis, Halomonas, and Crossiella, and to the two fungal genera Engyodontium and Teratosphaeria were present. In conclusion, we demonstrated the presence of abundant biofilm at efflorescence salt on the walls of the shelter; that was increased in quantity and diversity in spring.