Showing papers in "Archives of Microbiology in 2018"

Insights into the human oral microbiome.

Abstract: Human oral cavity harbors the second most abundant microbiota after the gastrointestinal tract. The expanded Human Oral Microbiome Database (eHOMD) that was last updated on November 22, 2017, contains the information of approximately 772 prokaryotic species, where 70% is cultivable, and 30% belong to the uncultivable class of microorganisms along with whole genome sequences of 482 taxa. Out of 70% culturable species, 57% have already been assigned to their names. The 16S rDNA profiling of the healthy oral cavity categorized the inhabitant bacteria into six broad phyla, viz. Firmicutes, Actinobacteria, Proteobacteria, Fusobacteria, Bacteroidetes and Spirochaetes constituting 96% of total oral bacteria. These hidden oral micro-inhabitants exhibit a direct influence on human health, from host’s metabolism to immune responses. Altered oral microflora has been observed in several diseases such as diabetes, bacteremia, endocarditis, cancer, autoimmune disease and preterm births. Therefore, it becomes crucial to understand the oral microbial diversity and how it fluctuates under diseased/perturbed conditions. Advances in metagenomics and next-generation sequencing techniques generate rapid sequences and provide extensive information of inhabitant microorganisms of a niche. Thus, the retrieved information can be utilized for developing microbiome-based biomarkers for their use in early diagnosis of oral and associated diseases. Besides, several apex companies have shown keen interest in oral microbiome for its diagnostic and therapeutic potential indicating a vast market opportunity. This review gives an insight of various associated aspects of the human oral microbiome.

A review of metabolic potential of human gut microbiome in human nutrition.

Abstract: The human gut contains a plethora of microbes, providing a platform for metabolic interaction between the host and microbiota. Metabolites produced by the gut microbiota act as a link between gut microbiota and its host. These metabolites act as messengers having the capacity to alter the gut microbiota. Recent advances in the characterization of the gut microbiota and its symbiotic relationship with the host have provided a platform to decode metabolic interactions. The human gut microbiota, a crucial component for dietary metabolism, is shaped by the genetic, epigenetic and dietary factors. The metabolic potential of gut microbiota explains its significance in host health and diseases. The knowledge of interactions between microbiota and host metabolism, as well as modification of microbial ecology, is really beneficial to have effective therapeutic treatments for many diet-related diseases in near future. This review cumulates the information to map the role of human gut microbiota in dietary component metabolism, the role of gut microbes derived metabolites in human health and host-microbe metabolic interactions in health and diseases.

Smoking and the intestinal microbiome.

Abstract: Studies are emerging alluding to the role of intestinal microbiome in the pathogenesis of diseases. Intestinal microbiome is susceptible to the influence of environmental factors such as smoking, and recent studies have indicated microbiome alterations in smokers. The aim of the study was to review the literature regarding the impact of smoking on the intestinal microbiome. A literature review of publications in PUBMED was performed using combinations of the terms "Intestinal/Gut/Gastrointestinal/Colonic" with "Microbiome/Microbiota/Microbial/Flora" and "Smoking/Smoker/Tobacco". We selected studies that were published between the years 2000 and 2016 as our inclusion criteria. Observational and interventional studies suggest that the composition of intestinal microbiome is altered due to smoking. In these studies, Proteobacteria and Bacteroidetes phyla were increased, as well as the genera of Clostridium, Bacteroides and Prevotella. On the other hand, Actinobacteria and Firmicutes phyla as well as the genera Bifidobacteria and Lactococcus were decreased. Smoking also decreased the diversity of the intestinal microbiome. Mechanisms that have been suggested to explain the effect of smoking on intestinal microbiome include: oxidative stress enhancement, alterations of intestinal tight junctions and intestinal mucin composition, and changes in acid-base balance. Interestingly, some smoking-induced alterations of intestinal microbiome resemble those demonstrated in conditions such as inflammatory bowel disease and obesity. Further studies should be performed to investigate this connection. Smoking has an effect on intestinal microbiome and is suggested to alter its composition. This interaction may contribute to the development of intestinal and systemic diseases, particularly inflammatory bowel diseases.

Mechanisms and improvement of acid resistance in lactic acid bacteria

Abstract: Lactic acid bacteria (LAB) can take advantage of fermentable carbohydrates to produce lactic acid. They are proverbially applied in industry, agricultural production, animal husbandry, food enterprise, pharmaceutical engineering and some other important fields, which are closely related to human life. For performing the probiotic functions, LAB have to face the low pH environment of the gastrointestinal tract. Therefore, acid resistance of LAB is of great importance not only for their own growth, but also for fermentation and preparation of probiotic products. Recent research studies on acid resistance mechanisms of LAB are mainly focused on neutralization process, biofilm and cell density, proton pump, protection of macromolecules, pre-adaptation and cross-protection, and effect of solutes. In this context, biotechnological strategies such as synthetic biology, genome shuffling, high pressure homogenization and adaptive laboratory evolution were also used to improve the acid resistance of LAB to respond to constantly changing low pH environment.

The diversity of sulfate-reducing bacteria in the seven bioreactors.

Abstract: Anaerobic technology has a wide scope of application in different areas such as manufacturing, food industry, and agriculture. Nowadays, it is mainly used to produce electrical and thermal energy from crop processing, solid waste treatment or wastewater treatment. More intensively, trend nowadays is usage of this technology biodegradable and biomass waste processing and biomethane or hydrogen production. In this paper, the diversities of sulfate-reducing bacteria (SRB) under different imputed raw material to the bioreactors were characterized. These diversities at the beginning of sampling and after cultivation were compared. Desulfovibrio, Desulfobulbus, and Desulfomicrobium genus as dominant among sulfate reducers in the bioreactors were detected. The Desulfobulbus species were dominant among other SRB genera before cultivation, but these bacteria were detected only in three out of the seven bioreactors after cultivation dominant.

Microbiological studies of hot springs in India: a review

Abstract: The earliest microbiological studies on hot springs in India date from 2003, a much later date compared to global attention in this striking field of study. As of today, 28 out of 400 geothermal springs have been explored following both culturable and non-culturable approaches. The temperatures and pH of the springs are 37–99 °C and 6.8–10, respectively. Several studies have been performed on the description of novel genera and species, characterization of different bio-resources, metagenomics of hot spring microbiome and whole genome analysis of few isolates. 17 strains representing novel species and many thermostable enzymes, including lipase, protease, chitinase, amylase, etc. with potential biotechnological applications have been reported by several authors. Influence of physico-chemical conditions, especially that of temperature, on shaping the hot spring microbiome has been established by metagenomic investigations. Bacteria are the predominant life forms in all the springs with an abundance of phyla Firmicutes, Proteobacteria, Actinobacteria, Thermi, Bacteroidetes, Deinococcus-Thermus and Chloroflexi. In this review, we have discussed the findings on all microbiological studies that have been carried out to date, on the 28 hot springs. Further, the possibilities of extrapolating these studies for practical applications and environmental impact assessment towards protection of natural ecosystem of hot springs have also been discussed.

Revealing strategies of quorum sensing in Azospirillum brasilense strains Ab-V5 and Ab-V6

Abstract: Azospirillum brasilense is an important plant-growth promoting bacterium (PGPB) that requires several critical steps for root colonization, including biofilm and exopolysaccharide (EPS) synthesis and cell motility. In several bacteria these mechanisms are mediated by quorum sensing (QS) systems that regulate the expression of specific genes mediated by the autoinducers N-acyl-homoserine lactones (AHLs). We investigated QS mechanisms in strains Ab-V5 and Ab-V6 of A. brasilense, which are broadly used in commercial inoculants in Brazil. Neither of these strains carries a luxI gene, but there are several luxR solos that might perceive AHL molecules. By adding external AHLs we verified that biofilm and EPS production and cell motility (swimming and swarming) were regulated via QS in Ab-V5, but not in Ab-V6. Differences were observed not only between strains, but also in the specificity of LuxR-type receptors to AHL molecules. However, Ab-V6 was outstanding in indole acetic acid (IAA) synthesis and this molecule might mimic AHL signals. We also applied the quorum quenching (QQ) strategy, obtaining transconjugants of Ab-V5 and Ab-V6 carrying a plasmid with acyl-homoserine lactonase. When maize (Zea mays L.) was inoculated with the wild-type and transconjugant strains, plant growth was decreased with the transconjugant of Ab-V5-confirming the importance of an AHL-mediated QS system-but did not affect plant growth promotion by Ab-V6.

Changes in intestinal microbiota of Bufo gargarizans and its association with body weight during metamorphosis

Abstract: The assembly of intestinal microbial communities can play major roles in animal development. We hypothesized that intestinal microbial communities could mirror the developmental programs of amphibian metamorphosis. Here, we surveyed the morphological parameters of the body and intestine of Bufo gargarizans at varying developmental stages and inventoried the intestinal microbial communities of B. gargarizans at four key developmental stages via 16S rDNA gene sequencing. Firstly, our survey showed that during metamorphosis, body weight and intestinal weight were reduced by 56.8 and 91.8%, respectively. Secondly, the gut bacterial diversity of B. gargarizans decreased with metamorphosis and the composition of the tadpoles' intestinal microbiota varied across metamorphosis. Compared to aquatic larvae, terrestrial juveniles showed major shifts in microbial composition, including reduction in Proteobacteria and Actinobacteria, increases in Bacteroidetes and Fusobacteria, and the appearance of Verrucomicrobia. Firmicutes in four developmental stages showed similar abundance at the phylum level, but in each stage was driven by distinct genera. Enterobacter, Aeromonas, Mucinivorans and Bacteroides also changed in abundance and were found to be significantly correlated with loss of body or intestinal tissue during metamorphosis. These results indicate a shift in intestinal microbial community composition throughout amphibian metamorphosis.

The influence of surface microbial diversity and succession on microbiologically influenced corrosion of steel in a simulated marine environment

Abstract: To explore how a succession of bacteria grown on steel coupons in a marine environment can influence their corrosion process, we designed a microcosm in laboratory to evaluate corrosion kinetics and microbial diversity over 30 days. The results described a clear influence of corrosion by a succession of different bacterial groups. During the initial period, 2–7 days, a sharp increase in the rate of corrosion was detected accompanied by the presence of Alteromonadaceae, Vibrionaceae, Oceanospirillaceae, Rhodobacteraceae, Rhodospirillaceae and Flavobacteriaceae bacteria families. After 15 days, representatives of families Piscirickettsiaceae and Pseudomonadaceae were also described, accompanied by a continuous corrosion process over the coupons. After 30 days, there was a sudden change in the profile of the bacteria present on the steel coupons, with a prevalence of Halomonadaceae family species, and establishment and continuity of the corrosion process by the biofilm grown on the coupons. The results describe differences in microbial diversity over the time, highlighting certain bacterial lithotrophic species that persisted for most of the experiment, through a complex association between bacteria and metal surfaces, which can be a new starting point for development and maintenance of a favorable microenvironment to accelerate corrosion processes.

Analysis of the succession of structure of the bacteria community in soil from long-term continuous cotton cropping in Xinjiang using high-throughput sequencing

Abstract: The present study aimed to identify the structural succession of the bacteria community in soil during long-term continuous cotton cropping and its relationship with continuous cropping obstacles in Xinjiang, China. High-throughput sequencing was used to analyze and compare the composition of the bacterial community in the soil at the cotton root zone after years of continuous cotton cropping and crop rotation over 30 years of cultivation. Cotton cultivation increased the structural diversity of the bacterial community, among which the populations of Actinobacteria, Acidobacteria, Firmicutes, Nitrospirae, and Chloroflexi changed considerably. A 0-year sample and samples after continuous short- and long-term cropping, along with some with crop rotation, were gathered into three individual clusters. The findings of the rotation sample were similar to those of the sample of continuous long-term cropping. Cropping is the main cause of changes in the structure of the bacteria community; however, the new structure formed under continued duress of both long-term cotton cultivation and the associated farming methods gradually stabilizes after 10 years of repeated fluctuations. Crop rotation can lead to the rapid recovery of some species of soil bacteria.

Prodigiosin pigment of Serratia marcescens is associated with increased biomass production

Abstract: Serratia marcescens is a gram-negative, facultatively-anaerobic bacterium and opportunistic pathogen which produces the red pigment prodigiosin. We employed both batch culture and chemostat growth methods to investigate prodigiosin function in the producing organism. Pigmentation correlated with an increased rate of ATP production during population lag phase. Results with a lacZ transcriptional fusion to the prodigiosin (pig) biosynthetic operon revealed that operon transcription is activated by low cellular levels of ATP at high cell density. Furthermore, these data enabled estimation of the ATP per cell minimum value at which the operon is induced. Pigmented cells were found to accumulate ATP more rapidly and to multiply more quickly than non-pigmented cells during the high density growth phase. Finally, results with both batch and chemostat culture revealed that pigmented cells grow to approximately twice the biomass yield as non-pigmented S. marcescens bacteria. Prodigiosin production may, therefore, provide a growth advantage at ambient temperatures.

Antioxidant activity and induction of mechanisms of resistance to stresses related to the inoculation with Azospirillum brasilense

Abstract: We investigated the effects of Azospirillum brasilense strains Ab-V5 and Ab-V6 in the induction of mechanisms of systemic acquired resistance (SAR) and induced system resistance (ISR) on maize (Zea mays L.) plants. Under normal growth conditions, the treatments consisted of the standard inoculation of cells at sowing, and leaf spray of cells or their metabolites at the V2.5 growth stage; under saline stress (170 mM NaCl), the treatment consisted of standard single and co-inoculation of A. brasilense and Rhizobium tropici. The main compounds in the Azospirillum metabolites were identified as indole-3-acetic acid (IAA) and salicylic acid (SA). Under normal conditions, A. brasilense cells applied at sowing or by leaf spray increased the activities of catalase (CAT), superoxide dismutase (SOD), and malondialdehyde (MDA) in leaves, and of ascorbate peroxidase (APX) in roots; however, interestingly, in general the highest activities were observed by leaf spray of metabolites. Under normal conditions, the highest levels of salicylic acid (SA) and jasmonic acid (JA) were achieved in leaves by leaf spray of metabolites, of SA in roots by leaf spray of cells, and of JA in roots by standard inoculation and leaf spray of metabolites. Under saline stress, plant protection occurred via SA and abscisic acid (ABA), but not JA. In general, inoculation resulted in further increases in SA in leaves and roots, and ABA in leaves. We hypothesize that A. brasilense confers protection to maize plants by simultaneous induction of JA and SA pathways, and, under saline stressing conditions, by SA and ABA pathways.

Endophytic fungus Paecilomyces formosus LHL10 produces sester-terpenoid YW3548 and cyclic peptide that inhibit urease and α-glucosidase enzyme activities

Abstract: Endophytic fungi have been used to obtain novel bioactive secondary metabolites with potential applications in medical and agricultural sectors, which can also act as lead targets for pharmaceutical and medicinal potential. In the present study, the endophytic fungus Paecilomyces formosus LHL10 isolated from the root of cucumber plant was tested for its enzyme inhibitory potential. The ethyl acetate (EtOAc) extract of LHL10 was screened for its inhibitory effect on acetylcholinesterase (AChE), α-glucosidase, urease, and anti-lipid peroxidation. The findings suggest that the EtOAc extract from LHL10 possesses significant inhibitory potential against urease and α-glucosidase. The EtOAc extract was thus, subjected to advanced column chromatographic techniques for the isolation of pure compounds. The structure elucidation was carried out through spectroscopic analysis and comparison with literature data, and these compounds were confirmed as known a sester-terpenoid (1) and a known cyclic peptide (2). The enzyme inhibition bioassay indicated that Compounds 1 and 2 exhibited remarkable inhibitory rate against α-glucosidase and urease, with an IC50 value of 61.80 ± 5.7, 75.68 ± 6.2 and 74.25 ± 4.3, 190.5 ± 10.31 µg/g, respectively. Thus, the current study concludes the enzyme inhibitory potential of endophyte LHL10 and provides the basis for further investigations of bioactive compounds, which could be used as potent drugs for enzyme inhibition.

Bradyrhizobium forestalis sp. nov., an efficient nitrogen-fixing bacterium isolated from nodules of forest legume species in the Amazon

Abstract: Three strains of nitrogen-fixing bacteria isolated from nodules of Inga sp. (INPA54BT) and Swartzia sp. (INPA86A and INPA01-91A) in soils under native forest in the Brazilian Amazon were previously identified as belonging to the Bradyrhizobium genus. In this study, these strains were characterized using a polyphasic approach to establish their taxonomic position. The three strains shared more than 99.5% sequence similarity of the 16S rRNA gene with the type strains of five Bradyrhizobium species (B. japonicum USDA 6T, B. liaoningense LMG 18230T, B. ottawaense OO99T, B. subterraneum 58 2-1T and B. yuanmingense LMG 21827T). However, multilocus sequence analysis of two (recA and glnII) or three (atpD, gyrB, and recA) housekeeping genes indicated that these three strains represent a new Bradyrhizobium species, which is closely related to B. subterraneum 58 2-1T and B. yuanmingense LMG 21827T. DNA–DNA hybridization values between INPA54BT and B. subterraneum 58 2-1T and B. yuanmingense LMG 21827T were only 41.5 and 30.9%, respectively. Phenotypic characterization also allowed the differentiation of the novel species from B. subterraneum 58 2-1T and B. yuanmingense LMG 21827T. In the phylogenetic analysis of the nodC and nifH genes, the three strains showed similar sequences that were divergent from those of type strains of all Bradyrhizobium species. We concluded that these strains represent a novel species, for which the name Bradyrhizobium forestalis is proposed, with INPA54BT (= LMG 10044T) as type strain. The G+C content in the DNA of INPA54BT is 63.7 mol%.

Global invasive Cochliobolus species: cohort of destroyers with implications in food losses and insecurity in the twenty-first century.

Abstract: Matching the global food demand by 2050 and to ensure the stability of food security in over than 99 countries, it is necessary to scale up the production of food such as sorghum, wheat, rice, maize and sugarcane which are however natural hosts of Cochliobolus species. Cochliobolus species major epidemics such as the Great Bengal famine, Southern corn leaf blight, and Northern leaf spot blight were associated with substantial economic losses in the past decades. Thus, there is an urgent need to establish a specific coordinated global surveillance program for the migration of invasive Cochliobolus species, planning contextual control programs engaging all agricultural stakeholders and information sharing in real time for prevention of disastrous Cochliobolus disease outbreak effects. We discuss pertinent outcome of interactions of cash crops with Cochliobolus species having devastating impact on the livelihood of farmers and food security. While post-genomic era elucidated prominent differences among Cochliobolus heterostrophus, C. carbonum, C. victoriae, C. lunatus and C. miyabeanus, their destructive potentials and implications in food losses remained unearthed. Intriguingly, the annual colossal losses caused by Cochliobolus species in the production perspective of sorghum, wheat, rice, maize, cassava and soybean is estimated over 10 billion USD worldwide. This paper provides a comprehensive analysis of the invasive Cochliobolus species distribution and diversity, evolving pathogenicity, persistent diseases, threats and epidemics, consequences on food crops production and increasing global food insecurity issues.

Isolation and characterization of a novel bacteriophage infecting Vibrio alginolyticus

Abstract: Vibrio alginolyticus is a common marine bacterium implicated in disease outbreaks in marine farmed fish and invertebrates. Due to the inappropriate use of antibiotics in aquaculture, alternative therapies have been proposed. One of the most promising options is the use of lytic bacteriophages to control pathogenic bacteria. This work describes the isolation and characterization of a lytic phage (VEN) against a V. alginolyticus strain (V2) isolated from a disease outbreak in common dentex (Dentex dentex) cultured at the Hellenic Centre for Marine Research (HCMR) in Crete, Greece. The bacteriophage is morphologically similar to phages from Podoviridae family and remained stable for 1 year at 4 °C and over 1 h when kept at 50 °C. VEN was able to lyse the host bacteria at several multiplicity of infection (MOI) (0.1–100) in liquid cultures. However, it was unable to infect other V. alginolyticus strains. Its genome consists of 44,603 bp with a GC content of 43.5%, while sequence analysis revealed the presence of 54 potential ORFs with a T7-like genomic organization. Almost 65% of the predicted ORFs presented homology with proteins of the vibriophages Vc1 and phi-A318 infecting Vibrio cyclitrophicus and Vibrio alginolyticus, respectively. Phylogenetic analysis applying the amino acid sequence of the large terminase subunit confirmed the close relationship of these phages. Furthermore, the comparison of the RNA polymerase of these phages revealed that the motifs A, B and C related to the catalytic activity and the recognition loop related to promotor identification were also conserved. VEN has an obligate lytic life cycle demonstrated by experimental data and genomic analysis. These results suggest that VEN may provide a good candidate to control recurrent diseases caused by V. alginolyticus at HCMR.

Rapid molecular identification and differentiation of common Salmonella serovars isolated from poultry, domestic animals and foodstuff using multiplex PCR assay.

Abstract: Salmonella is widely distributed throughout the world and can be found in poultry industry, animal breeding centers, food and feedstuffs of all geographical regions. This study was conducted to determine and identify Salmonella serovars isolated from poultry, calves and foodstuffs (poultry and animals products such as egg and meat). A total of one hundred isolates of Salmonella serovars including Salmonella Typhimurium, Salmonella Enteritidis, Salmonella Infantis, Salmonella Gallinarum and Salmonella Pullorum consecutively were subjected to the conventional culture, biochemical and serological assays. The utility of molecular multiplex PCR was investigated to identify and differentiate among five Salmonella serovars which were identified according to the presence of rfbJ, fljB, invA, and fliC genes in S. Typhimurium, sefA, invA and spv genes in Salmonella Enteritidis, fljB, fliC and invA genes in Salmonella Infantis, hut and slgC genes in both Salmonella Gallinarum and Salmonella Pullorum and speC gene specifically in Salmonella Gallinarum. Biochemical assays and serotyping are complicated to directly differentiate between Salmonella Gallinarum and Salmonella Pullorum because of their antigenic similarity. According to the results, Multiplex PCR can be considered as simple, rapid, accurate and useful test to identify and differentiate among Salmonella serovars.

Production of indoleacetic acid by strains of the epiphytic bacteria Neptunomonas spp. isolated from the red alga Pyropia yezoensis and the seagrass Zostera marina

Abstract: Neptunomonas sp. BPy-1 is an epiphytic bacterium isolated from in vitro culture of the red alga Pyropia yezoensis. It uses ethanol as a sole carbon source and promotes the growth of host alga. A related bacterium, Neptunomonas sp. BZm-1, was isolated from leaves of Zostera marina found in the Yatsushiro Sea (Japan). BZm-1 showed 99% 16S rRNA sequence identity with Neptunomonas sp. BPy-1. Similar to BPy-1, BZm-1 grew in artificial seawater (ASW) medium containing ethanol or butanol. When thalli were treated with a multi-enzyme cleaner, the growth of treated thalli was retarded, but the addition of BZm-1 to the medium promoted growth. To explore the benefits of epiphytic bacteria, indoleacetic acid (IAA) production by isolated bacteria was examined under conditions of limited nutrients. Salkowski assays and GC-MS analysis revealed that both BZm-1 and BPy-1 excreted IAA during growth in ASW medium containing glucose or ethanol in the presence of tryptophan. In ASW medium containing tryptophan but lacking a carbon source, neither isolate grow, but produced IAA. ASW medium includes nitrate as the sole nitrogen source. In the absence of carbon source, different nitrogen forms in the presence of tryptophan did not affect IAA production by the two isolates. These findings indicate that IAA production by the two isolates is strictly dependent on tryptophan but less affected by carbon and nitrogen sources. Based on the different origins of BPy-1 and BZm-1, this mode of IAA production seems to be conserved among relatives of BPy-1.

Inhibition of sialidase activity and cellular invasion by the bacterial vaginosis pathogen Gardnerella vaginalis

Abstract: Bacterial vaginosis is a genital tract infection, thought to be caused by transformation of a lactobacillus-rich flora to a dysbiotic microbiota enriched in mixed anaerobes. The most prominent of these is Gardnerella vaginalis (GV), an anaerobic pathogen that produces sialidase enzyme to cleave terminal sialic acid residues from human glycans. Notably, high sialidase activity is associated with preterm birth and low birthweight. We explored the potential of the sialidase inhibitor Zanamavir against GV whole cell sialidase activity using methyl–umbelliferyl neuraminic acid (MU-NANA) cleavage assays, with Zanamavir causing a 30% reduction in whole cell GV sialidase activity (p < 0.05). Furthermore, cellular invasion assays using HeLa cervical epithelial cells, infected with GV, demonstrated that Zanamivir elicited a 50% reduction in cell association and invasion (p < 0.05). Our data thus highlight that pharmacological sialidase inhibitors are able to modify BV-associated sialidase activity and influence host–pathogen interactions and may represent novel therapeutic adjuncts.

Fecal microbiota of lambs fed purple prairie clover (Dalea purpurea Vent.) and alfalfa (Medicago sativa).

Abstract: The present study assessed the effect of purple prairie clover (PPC) and PPC condensed tannins (CT) on the fecal microbiota of lambs using high-throughput 16S rRNA gene pyrosequencing. A total of 18 individual lambs were randomly divided into three groups and fed either green chop alfalfa (Alf), a 40:60 (DM basis; Mix) mixture of Alf and PPC, or Mix supplemented with polyethylene glycol (Mix-P) for 18 days. Fecal samples were collected on days 13 through 18 using digital rectal retrieval. The DNA of fecal samples was extracted and the microbial 16S rRNA gene amplicons were sequenced using 454 pyrosequencing. Regardless of diet, the bacterial community was dominated by Firmicutes and Bacteroidetes with many sequences unclassified at the genus level. Forage type and CT had no effect on the fecal microbial composition at the phylum level or on α-diversity. Compared to the Alf diet, the Mix diet reduced the relative abundance of Akkermansia (P = 0.03) and Asteroleplasma (P = 0.05). Fecal microbial populations in Alf and Mix-P clustered separately from each other when assessed using unweighted UniFrac (P < 0.05). These results indicate that PPC CT up to 36 g/kg DM in the diet had no major effect on fecal microbial flora at the phyla level and exerted only minor effects on the genera composition of fecal microbiota in lambs.

Mechanism of arsenic resistance in endophytic bacteria isolated from endemic plant of mine tailings and their arsenophore production.

Abstract: Arsenic contamination is an important environmental problem around the world since its high toxicity, and bacteria resist to this element serve as valuable resource for its bioremediation. Aiming at searching the arsenic-resistant bacteria and determining their resistant mechanism, a total of 27 strains isolated from roots of Prosopis laevigata and Spharealcea angustifolia grown in a heavy metal-contaminated region in Mexico were investigated. The minimum inhibitory concentration (MIC) and transformation abilities of arsenate (As5+) and arsenite (As3+), arsenophore synthesis, arsenate uptake, and cytoplasmatic arsenate reductase (arsC), and arsenite transporter (arsB) genes were studied for these strains. Based on these results and the 16S rDNA sequence analysis, these isolates were identified as arsenic-resistant endophytic bacteria (AREB) belonging to the genera Arthrobacter, Bacillus, Brevibacterium, Kocuria, Microbacterium, Micrococcus, Pseudomonas, and Staphylococcus. They could tolerate high concentrations of arsenic with MIC from 20 to > 100 mM for As5+ and 10–20 mM for As3+. Eleven isolates presented dual abilities of As5+ reduction and As3+ oxidation. As the most effective strains, Micrococcus luteus NE2E1 reduced 94% of the As5+ and Pseudomonas zhaodongensis NM2E7 oxidized 46% of As3+ under aerobic condition. About 70 and 44% of the test strains produced arsenophores to chelate As5+ and As3+, respectively. The AREB may absorb arsenate via the same receptor of phosphate uptake or via other way in some case. The cytoplasmic arsenate reductase and alternative arsenate reduction pathways exist in these AREB. Therefore, these AREB could be candidates for the bioremediation process.

Genes involved in Beauveria bassiana infection to Galleria mellonella

Abstract: The ascomycete fungus Beauveria bassiana is a natural pathogen of hundreds of insect species and is commercially produced as an environmentally friendly mycoinsecticide. Many genes involved in fungal insecticide infection have been identified but few have been further explored. In this study, we constructed three transcriptomes of B. bassiana at 24, 48 and 72 h post infection of insect pests (BbI) or control (BbC). There were 3148, 3613 and 4922 genes differentially expressed at 24, 48 and 72 h post BbI/BbC infection, respectively. A large number of genes and pathways involved in infection were identified. To further analyze those genes, expression patterns across different infection stages (0, 12, 24, 36, 48, 60, 72 and 84 h) were studied using quantitative RT-PCR. This analysis showed that the infection-related genes could be divided into four patterns: highly expressed throughout the whole infection process (thioredoxin 1); highly expressed during early stages of infection but lowly expressed after the insect death (adhesin protein Mad1); lowly expressed during early infection but highly expressed after insect death (cation transporter, OpS13); or lowly expressed across the entire infection process (catalase protein). The data provide novel insights into the insect–pathogen interaction and help to uncover the molecular mechanisms involved in fungal infection of insect pests.

Rhodanobacter ginsengiterrae sp. nov., an antagonistic bacterium against root rot fungal pathogen Fusarium solani , isolated from ginseng rhizospheric soil

Abstract: A novel bacterium, designated DCY112T, was isolated from the rhizospheric soil of a ginseng-cultivated field in Gochang-gun, Republic of Korea. Based on 16S rRNA gene sequence analysis, this isolate was assigned to the genus Rhodanobacter and is closely related to Rhodanobacter soli DCY45T (98.0%) and R. umsongensis GR24-2T (98.0%). Strain DCY112T is Gram-negative, catalase- and oxidase-positive, aerobic, non-motile, rod-shaped, and produces yellow-pigmented colonies on R2A medium. Q-8 was the predominant respiratory quinone. The major cellular fatty acids were iso-C15:0, iso-C17:0, and summed feature 9 (iso-C17:1 ω9c and/or 10-methyl-C16:0). The major polar lipids were phosphatidylglycerol (PG), phosphatidylethanolamine (PE), an unknown amino lipid (AL1), and an unidentified polar lipid (L3). The genomic DNA G + C content was 65.2 mol%. DNA–DNA homology values between strain DCY112T and related strains were lower than 55%. The low DNA relatedness data in combination with phenotypic and genotypic tests indicated that strain DCY112T could not be assigned to a recognized species. Strain DCY112T showed antagonistic activity against the fungal pathogen Fusarium solani (KACC 44891T), which causes ginseng root rot. The results of this study support that strain DCY112T is a novel species belonging to the genus Rhodanobacter, for which the name Rhodanobacter ginsengiterrae is proposed. The type strain is DCY112T (= KCTC 62018T = JCM 32167T).

Untapped bacterial diversity and metabolic potential within Unkeshwar hot springs, India.

Abstract: Hot springs support diverse and interesting groups of microorganisms adapted to extreme conditions and gaining attention in biotechnological applications. However, due to limitations of cultivation methods, a majority of such extremophiles remain uncultivated and unexplored. The advent of multiple cultivation conditions and specialized culture media could possibly aid to access the unexplored microbial portion of hot springs. In the present study, different media and isolation strategies were applied to isolate hitherto unexplored bacterial taxa in the water samples collected from Unkeshwar hot springs, India. Molecular, phylogenetic and predictive functional characterization of the isolated bacterial population was done using 16S rRNA sequencing coupled with Tax4Fun tools. Furthermore, representative isolates were screened for important enzymes (cellulase, xylanase, amylase, and protease) and heavy metal tolerance (chromium, arsenic) properties. A total of 454 bacterial isolates obtained were mapped into 57 unique bacterial genera and 4 different bacterial phyla. Interestingly, 37 genera not previously isolated from Indian hot springs, were isolated for the first time in the present study. However, most of these genera (23 out of 37) were reported only in metagenomics studies from Indian and global hot springs. Furthermore, around 14 genera not previously cultivated and not detected in metagenomics studies of hot springs are documented here. The metabolic potential was ascertained by determining the abundance of specific genes using in silico based Tax4Fun tool, which identified around 315 metabolic pathways for metabolism of carbohydrates, synthesis of secondary metabolites and degradation of xenobiotic compounds. Bioprospection study revealed that 33 and 25 bacterial genera were positive for enzyme production and resistance to the heavy metals, respectively. The present study revealed the advantages of cultivation methods using a comprehensive multiple isolation approach for exploring untapped and unique bacterial diversity, and also utilities for various biotechnological and environmental applications.

Quorum sensing inhibitors: can endophytes be prospective sources?

Abstract: Endophytes are microbes which reside inside the plant tissues asymptomatically or causing pathogenicity to the host plant for a brief period. Owing to their presence in a specialized niche, endophytes are capable of synthesizing diverse types of bioactive molecules. Continuous development of resistance mechanism by pathogens to the currently available health treatments and pharmaceuticals has led researchers to explore new therapeutic agents. Quorum sensing has a role in the development of microbial pathogenic traits including biofilm formation. Utilization of quorum sensing (QS) inhibitors in antivirulence approach against pathogenesis is one of the innovative strategies. Endophytic microbes provide a plethora of such required bioactive molecules. This review summarizes the bioprospecting of endophytic microbes for production of novel QS inhibitors. At the outset, an overview is presented about the QS and QS inhibition followed by a summary on the endophytes as a treasure trove of bioactive metabolites, particularly the QS inhibitors. Next, we have outlined screening, purification, production, and application of QS inhibitors starting from the isolation of endophytic microbes. There is huge prospect for endophytes in the domain of human healthcare and food industry, provided that we develop a comprehensive understanding of the biology of endophyte and its ecosystem.

Colistin causes profound morphological alteration but minimal cytoplasmic membrane perforation in populations of Escherichia coli and Pseudomonas aeruginosa.

Abstract: Whilst colistin (polymyxin E) represents the last mainstream treatment option for multidrug-resistant Gram-negative pathogens, details of its mechanism of action remain to be fully resolved. In this study, the effects of sub-inhibitory, inhibitory-bactericidal, and supra-bactericidal levels of colistin on the membrane integrity and morphology of Escherichia coli and Pseudomonas aeruginosa were investigated using potassium loss, flow cytometry, and scanning electron microscopy (SEM). Supra-bactericidal colistin concentrations induced just 4–12% intracellular potassium loss from bacteria after 24 h. Flow cytometry data suggested colistin might alter cell arrangement, and SEM confirmed the antibiotic causes bacterial aggregation. Filamentation was not detected in either species at any concentration or time-point up to 24 h. These results argue against the hypotheses that colistin kills bacteria by puncturing the cytoplasmic membrane or disrupting DNA synthesis. The colistin-induced bacterial aggregation detected has implications for the interpretation of MBC, time-kill, and other test results obtained with this antibiotic.

Antibacterial activity of monoacetylated alkyl gallates against Xanthomonas citri subsp. citri

Abstract: Asiatic citrus canker (ACC) is an incurable disease of citrus plants caused by the Gram-negative bacterium Xanthomonas citri subsp. citri (X. citri). It affects all the commercially important citrus varieties in the major orange producing areas around the world. Control of the pathogen requires recurrent sprays of copper formulations that accumulate in soil and water reservoirs. Here, we describe the improvement of the alkyl gallates, which are potent anti-X. citri compounds, intended to be used as alternatives to copper in the control of ACC. Acetylation of alkyl gallates increased their lipophilicity, which resulted in potentiation of the antibacterial activity. X. citri exposed to the acetylated compounds exhibited increased cell length that is consistent with the disruption of the cell division apparatus. Finally, we show that inhibition of cell division is an indirect effect that seemed to be caused by membrane permeabilization, which is apparently the primary target of the acetylated alkyl gallates.

Dyadobacter flavus sp. nov. and Dyadobacter terricola sp. nov., two novel members of the family Cytophagaceae isolated from forest soil.

Abstract: Two strains of bacteria designated strains S-53T and A27T were isolated from forest soil and subjected to polyphasic characterization. Cells were aerobic, Gram-staining-negative, catalase- and oxidase- positive, non-motile, non-spore-forming, rod-shaped, and yellow-pigmented. Flexirubin-type pigments were present. Both strains were positive for PNPG, hydrolysed casein, and tyrosine. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strains S-53T and A27T formed a lineage within the family Cytophagaceae that were distinct from various members of the genus Dyadobacter (98.9–93.2% sequence similarity). Closest member for strain S-53T was Dyadobacter jejuensis AM1R11T (95.7%) and for A27T Dyadobacter endophyticus 65T (98.9%). The predominant respiratory quinone was MK-7 for both strains. The major polar lipid for both strains was phosphatidylethanolamine. The major cellular fatty acids for both strains were summed feature 3 (C16:1ω7c and/or C16:1ω6c), iso-C15:0, C16:1ω5c, and C16:0. The DNA G+C content of strains ranges from 46.5 to 48.7 mol%. On the basis of phenotypic, genotypic, chemotaxonomic, and phylogenetic analysis, both strains S-53T and A27T represent a novel member in the genus Dyadobacter, for which the name Dyadobacter flavus sp. nov. and Dyadobacter terricola sp. nov. are proposed, respectively. The type strain of D. flavus is S-53T (= KEMB 9005-541T = KACC 19149T = NBRC 112681T) and type strain of D. terricola is A27T (= KEMB 9005-524T = KACC 19147T = NBRC 112680T).

Bacteriocinogenic properties of Escherichia coli P2C isolated from pig gastrointestinal tract: purification and characterization of microcin V

Abstract: The aim of this study was to isolate and investigate the bacteriocinogenic and probiotic potential of new Gram-negative isolates. Of 22 bacterial isolates from pig intestine and chicken crops, ten isolates had demonstrated a good activity, and the most potent five strains were identified as four E. coli and one as Proteus sp. No virulence factors were detected for E. coli strains isolated from pig intestine. The semi-purified microcins proved to be resistant to temperature and pH variation, but sensitive to proteolytic enzymes. Of particular interest, strain E. coli P2C was the most potent, free of virulence genes and sensitive to tested antibiotics. Purification procedure revealed the presence of a single pure peak having a molecular mass of 8733.94 Da and matching microcin V (MccV). The sequence obtained by LC–MS/MS confirmed the presence of MccV. Purified MccV showed a good activity against pathogenic coliforms, especially E. coli O1K1H7 involved in avian colibacillosis. The present study provides evidence that E. coli strains isolated from pig intestine produce microcin-like substances. E. coli P2C is a safe MccV producer that could be a good candidate for its application as novel probiotic strain to protect livestock and enhance growth performance.

A capsule/lipopolysaccharide/MLST genotype D/L6/ST11 of Pasteurella multocida is likely to be strongly associated with swine respiratory disease in China

Abstract: Pasteurella multocida is a leading cause of respiratory disease in pigs worldwide. In this study, we determined the genetic characteristics of 115 P. multocida isolates from the lungs of pigs with respiratory disease in China in 2015 using capsular typing, lipopolysaccharide (LPS) genotyping, and virulence genotyping based on the detection of virulence-associated genes. The results showed that the isolates belonged to three capsular types: A (49.6%), D (46.1%), and nontypable (4.3%); and two LPS genotypes: L3 (22.6%) and L6 (77.4%). When combining the capsular types with the LPS genotypes, a genotype group D: L6 (46.1%) was the most prevalent among the strains. Among the 23 virulence-associated genes detected in this study, a small number of them displayed a certain level of "genotype-preference". We found that pfhA, hgbA, and hgbB had a close association with P. multocida LPS genotypes, while tadD was more associated with P. multocida capsular types. In addition, multilocus sequence typing (MLST) on 40 P. multocida isolates identified four sequence types: ST3, ST10, ST11, and ST16, and the distribution of ST11 was significantly higher than the other MLST genotypes. Interestingly, all of the ST11 isolates detected in this study were genotype D: L6 strains and they were 100% positive for hgbB. Our data suggest that a capsule/LPS/MLST genotype D/L6/ST11 is likely to be strongly associated with respiratory clinical manifestation of the disease in pigs.