Secretion systems play a critical role in resistance to predation by Bdellovibrio bacteriovorus.

Bdellovibrio bacteriovorus, a Gram-negative predatory bacterium belonging to the Bdellovibrio and like organisms (BALOs), predates on Gram-negative bacteria. BALO strains differ in prey range but so far, the genetic basis of resistance against BALO predation is hardly understood. We developed a loss-of-function approach to screen for sensitive mutants in a library of strain M6, a predation-resistant strain of the plant pathogen Acidovorax citrulli. The screen is based on tracking the growth of a B. bacteriovorus strain expressing the fluorescent reporter Tdtomato in mutant pools to reveal predation-sensitive variants. Two independent loci were identified in mutant strains exhibiting significant levels of susceptibility to the predator. Genes in the two loci were analysed using both protein sequence homology and protein structure modeling. Both were secretion-related proteins and thus associated to the bacterial cell wall. Successful complementation of gspK, a gene encoding for a minor pseudopilin protein confirmed the involvement of the type II secretion system in A. citrulli M6 resistance. This proof of concept study shows that our approach can identify key elements of the BALO-prey interaction, and it validates the hypothesis that mutational changes in a single gene can drastically impact prey resistance to BALO predation.

Ramlibacter terrae sp. nov. and Ramlibacter montanisoli sp. nov., Isolated from Soil.

Two gram-negative, catalase-positive, strictly aerobic, and white colony-forming bacteria, strains H242T and B156T, were isolated from soil in South Korea. Cells of strain H242T were oxidase-positive and non-motile short rods, while those of strain B156T were oxidase-negative and long non-motile rods. Ubiquinone-8 was identified as the sole isoprenoid quinone in both strains. C16:0, cyclo-C17:0, and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) and phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol were identified in both strains as the major cellular fatty acids and polar lipids, respectively. The DNA G+C contents of strains H242T and B156T were 69.4 mol% and 69.3 mol%, respectively. Phylogenetic analyses based on 16S rRNA and 92 concatenated core gene sequences revealed that strains H242T and B156T formed distinct phylogenic lineages from other Ramlibacter type strains. The DNA-DNA hybridization (DDH) value between strains H242T and B156T was 24.6%. Strains H242T and B156T were most closely related to Ramlibacter ginsenosidimutans BXN5-27T and Ramlibacter monticola G-3-2T with 98.4% and 98.6% 16S rRNA gene sequence similarities, respectively. Digital DDH values between strain H242T and R. ginsenosidimutans and between strain B156T and R. monticola were 23.5% and 26.1%, respectively. Phenotypic, chemotaxonomic, and molecular analyses indicated that strains H242T and B156T represent two novel species of the genus Ramlibacter, for which the names Ramlibacter terrae sp. nov. and Ramlibacter montanisoli sp. nov., respectively, are proposed. The type strains of R. terrae and R. montanisoli are H242T (=KACC 21667 T =JCM 33922T) and B156T (=KACC 21665 T =JCM 33920T), respectively.

Response of intercropped barley and fenugreek to mono- and co-inoculation with Sinorhizobium meliloti F42 and Variovorax paradoxus F310 under contrasting agroclimatic regions.

In the present research, we aimed to select efficient rhizobia and plant growth-promoting rhizobacteria (PGPR) from fenugreek nodules and assess their performance as bio-inoculum for intercropped fenugreek and barley. Inoculation effects with selected bacteria were investigated firstly on fenugreek plants under greenhouse experiment and secondly on intercropped fenugreek and barley under three different agro-environmental conditions for two consecutive years. Sinorhizobium meliloti F42 was selected due to its ability to nodulate fenugreek and effectively improve plant growth. Among non-nodulating endophytic bacteria, Variovorax paradoxus F310 strain was selected regarding its plant growth-promoting traits showed in vitro and confirmed in vivo under greenhouse experiment. Field inoculation trials revealed a significant improvement in fenugreek nodulation (up to + 97%) as well as in soil enzymes activities (up to + 209%), shoot N content (up to + 18%), shoot dry weight (up to + 40%), photosynthetic assimilation (up to + 34%) and chlorophyll content of both intercropped plants in response to the mono-inoculation with Sinorhizobium meliloti F42, compared to the un-inoculated treatment at the SBR and JBS sites. Variovorax paradoxus F310 inoculation significantly increased shoot P content of both intercropped plants at the three experimental sites compared to the un-inoculated treatment (up to + 48%). It was shown that bacterial inoculation was more efficient at the low-rainfall region than the high-rainfall region. The co-inoculation with Sinorhizobium meliloti F42 and Variovorax paradoxus F310 resulted in a significant reduction in fenugreek nodulation and shoot N content. This survey showed the benefits of rhizobial and PGPR inoculation as efficient bio-inoculums to promote the cereal-legume intercropping system and highlights the influence of site-specific environmental factors on Rhizobium-PGPR-plant interactions.

A single bacterial genus maintains root growth in a complex microbiome.

Plants grow within a complex web of species that interact with each other and with the plant1-10. These interactions are governed by a wide repertoire of chemical signals, and the resulting chemical landscape of the rhizosphere can strongly affect root health and development7-9,11-18. Here, to understand how interactions between microorganisms influence root growth in Arabidopsis, we established a model system for interactions between plants, microorganisms and the environment. We inoculated seedlings with a 185-member bacterial synthetic community, manipulated the abiotic environment and measured bacterial colonization of the plant. This enabled us to classify the synthetic community into four modules of co-occurring strains. We deconstructed the synthetic community on the basis of these modules, and identified interactions between microorganisms that determine root phenotype. These interactions primarily involve a single bacterial genus (Variovorax), which completely reverses the severe inhibition of root growth that is induced by a wide diversity of bacterial strains as well as by the entire 185-member community. We demonstrate that Variovorax manipulates plant hormone levels to balance the effects of our ecologically realistic synthetic root community on root growth. We identify an auxin-degradation operon that is conserved in all available genomes of Variovorax and is necessary and sufficient for the reversion of root growth inhibition. Therefore, metabolic signal interference shapes bacteria-plant communication networks and is essential for maintaining the stereotypic developmental programme of the root. Optimizing the feedbacks that shape chemical interaction networks in the rhizosphere provides a promising ecological strategy for developing more resilient and productive crops.

The effects of exopolysaccharides and exopolysaccharide-producing Lactobacillus on the intestinal microbiome of zebrafish (Danio rerio).

BACKGROUND: Numerous studies have reported the health-promoting effects of exopolysaccharides (EPSs) in in vitro models; however, a functional evaluation of EPSs will provide additional knowledge of EPS-microbe interactions by in vivo intestinal microbial model. In the present study, high-throughput amplicon sequencing, short-chain fatty acid (SCFAs) and intestinal inflammation evaluation were performed to explore the potential benefits of exopolysaccharides (EPSs) and EPS-producing Lactobacillus (HNUB20 group) using the healthy zebrafish (Danio rerio) model. RESULTS: The results based on microbial taxonomic analysis revealed that the abundance of four genera, Ochrobactrum, Sediminibacterium, Sphingomonas and Sphingobium, were increased in the control group in comparison to HNUB20 group. Pelomonas spp. levels were significantly higher and that of the genera Lactobacillus and Brachybacterium were significantly decreased in EPS group compared with control group. PICRUSt based functional prediction of gut microbiota metabolic pathways indicated that significantly lower abundance was found for transcription, and membrane transport, whereas folding, sorting and degradation and energy metabolism had significantly higher abundance after HNUB20 treatment. Two metabolic pathways, including metabolism and endocrine functions, were more abundant in the EPS group than control group. Similar to the HNUB20 group, transcription was also decreased in the EPS group compared with the control group. However, SCFAs and immune indexes indicated EPS and HNUB20 performed limited efficacy in the healthy zebrafish. CONCLUSIONS: The present intestinal microbial model-based study indicated that EPSs and high-yield EPS-producing Lactobacillus can shake the structure of intestinal microbiota, but cannot change SCFAs presence and intestinal inflammation.

Microbial Species Coexistence Depends on the Host Environment.

Organisms and their resident microbial communities form a complex and mostly stable ecosystem. It is known that the specific composition and abundance of certain bacterial species affect host health and fitness, but the processes that lead to these microbial patterns are unknown. We investigate this by deconstructing the simple microbiome of the freshwater polyp Hydra We contrast the performance of its two main bacterial associates, Curvibacter and Duganella, on germfree hosts with two in vitro environments over time. We show that interactions within the microbiome but also the host environment lead to the observed species frequencies and abundances. More specifically, we find that both microbial species can only stably coexist in the host environment, whereas Duganella outcompetes Curvibacter in both in vitro environments irrespective of initial starting frequencies. While Duganella seems to benefit through secretions of Curvibacter, its competitive effect on Curvibacter depends upon direct contact. The competition might potentially be mitigated through the spatial distribution of the two microbial species on the host, which would explain why both species stably coexist on the host. Interestingly, the relative abundances of both species on the host do not match the relative abundances reported previously nor the overall microbiome carrying capacity as reported in this study. Both observations indicate that rare microbial community members might be relevant for achieving the native community composition and carrying capacity. Our study highlights that for dissecting microbial interactions the specific environmental conditions need to be replicated, a goal difficult to achieve with in vitro systems.IMPORTANCE This work studies microbial interactions within the microbiome of the simple cnidarian Hydra and investigates whether microbial species coexistence and community stability depend on the host environment. We find that the outcome of the interaction between the two most dominant bacterial species in Hydra's microbiome differs depending on the environment and results in a stable coexistence only in the host context. The interactive ecology between the host and the two most dominant microbes, but also the less abundant members of the microbiome, is critically important for achieving the native community composition. This indicates that the metaorganism environment needs to be taken into account when studying microbial interactions.

Temperature and Nutrient Levels Correspond with Lineage-Specific Microdiversification in the Ubiquitous and Abundant Freshwater Genus Limnohabitans.

Most freshwater bacterial communities are characterized by a few dominant taxa that are often ubiquitous across freshwater biomes worldwide. Our understanding of the genomic diversity within these taxonomic groups is limited to a subset of taxa. Here, we investigated the genomic diversity that enables Limnohabitans, a freshwater genus key in funneling carbon from primary producers to higher trophic levels, to achieve abundance and ubiquity. We reconstructed eight putative Limnohabitans metagenome-assembled genomes (MAGs) from stations located along broad environmental gradients existing in Lake Michigan, part of Earth's largest surface freshwater system. De novo strain inference analysis resolved a total of 23 strains from these MAGs, which strongly partitioned into two habitat-specific clusters with cooccurring strains from different lineages. The largest number of strains belonged to the abundant LimB lineage, for which robust in situ strain delineation had not previously been achieved. Our data show that temperature and nutrient levels may be important environmental parameters associated with microdiversification within the Limnohabitans genus. In addition, strains predominant in low- and high-phosphorus conditions had larger genomic divergence than strains abundant under different temperatures. Comparative genomics and gene expression analysis yielded evidence for the ability of LimB populations to exhibit cellular motility and chemotaxis, a phenotype not yet associated with available Limnohabitans isolates. Our findings broaden historical marker gene-based surveys of Limnohabitans microdiversification and provide in situ evidence of genome diversity and its functional implications across freshwater gradients.IMPORTANCELimnohabitans is an important bacterial taxonomic group for cycling carbon in freshwater ecosystems worldwide. Here, we examined the genomic diversity of different Limnohabitans lineages. We focused on the LimB lineage of this genus, which is globally distributed and often abundant, and its abundance has shown to be largely invariant to environmental change. Our data show that the LimB lineage is actually comprised of multiple cooccurring populations for which the composition and genomic characteristics are associated with variations in temperature and nutrient levels. The gene expression profiles of this lineage suggest the importance of chemotaxis and motility, traits that had not yet been associated with the Limnohabitans genus, in adapting to environmental conditions.

Motility and phototaxis of Gonium, the simplest differentiated colonial alga.

Green algae of the Volvocine lineage, spanning from unicellular Chlamydomonas to vastly larger Volvox, are models for the study of the evolution of multicellularity, flagellar dynamics, and developmental processes. Phototactic steering in these organisms occurs without a central nervous system, driven solely by the response of individual cells. All such algae spin about a body-fixed axis as they swim; directional photosensors on each cell thus receive periodic signals when that axis is not aligned with the light. The flagella of Chlamydomonas and Volvox both exhibit an adaptive response to such signals in a manner that allows for accurate phototaxis, but in the former the two flagella have distinct responses, while the thousands of flagella on the surface of spherical Volvox colonies have essentially identical behavior. The planar 16-cell species Gonium pectorale thus presents a conundrum, for its central 4 cells have a Chlamydomonas-like beat that provide propulsion normal to the plane, while its 12 peripheral cells generate rotation around the normal through a Volvox-like beat. Here we combine experiment, theory, and computations to reveal how Gonium, perhaps the simplest differentiated colonial organism, achieves phototaxis. High-resolution cell tracking, particle image velocimetry of flagellar driven flows, and high-speed imaging of flagella on micropipette-held colonies show how, in the context of a recently introduced model for Chlamydomonas phototaxis, an adaptive response of the peripheral cells alone leads to photoreorientation of the entire colony. The analysis also highlights the importance of local variations in flagellar beat dynamics within a given colony, which can lead to enhanced reorientation dynamics.

Prevalence of Acidovorax citrulli in Commercial Cucurbit Seedlots During 2010-2018 in China.

Acidovorax citrulli is the causal agent of bacterial fruit blotch (BFB), a serious threat to cucurbit fruit and seed production worldwide. In recent years, the BFB has spread to many areas of China, mainly via the inadvertent distribution of contaminated commercial seeds. To assess the prevalence of seedborne A. citrulli in commercial watermelon and other cucurbitaceous seedlots in China, a 9-year survey was conducted between 2010 and 2018. A total of 4,839 seedlots of watermelon and other cucurbitaceous species were collected from 13 major seed production areas of China and tested by a semiselective media-based colony PCR technique for A. citrulli. Overall, A. citrulli was detected in 18.00% (871/4,839) of all cucurbitaceous seedlots. The bacterium was detected in 21.59% (38/176), 19.19% (33/172), 23.44% (214/913), 40.76% (247/606), 13.28% (85/640), 15.40% (95/617), 13.25% (73/551), 8.03% (48/598), and 6.71% (38/566) of all commercial seedlots tested from the 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, and 2018 growing seasons, respectively. Additionally, the prevalence of A. citrulli in cucurbit seedlots was determined for different seed production areas. The prevalence of A. citrulli in cucurbitaceous seedlots produced in Xinjiang, Gansu, Ningxia, Inner Mongolia, and 9 other provinces was 18.76% (582/3103), 26.34% (103/391), 21.47% (82/382), 11.11% (14/126), and 10.75% (90/837), respectively. This is the first survey for A. citrulli in commercial cucurbit seeds in China, and the relatively high prevalence suggests that commercial seeds represent a substantial source of primary inoculum that can threaten cucurbit seed and fruit production in China.

Light on the cell cycle of the non-photosynthetic bacterium Ramlibacter tataouinensis.

Ramlibacter tataouinensis TTB310, a non-photosynthetic betaproteobacterium isolated from a semi-arid region of southern Tunisia, forms both rods and cysts. Cysts are resistant to desiccation and divide when water and nutrients are available. Rods are motile and capable of dissemination. Due to the strong correlation between sunlight and desiccation, light is probably an important external signal for anticipating desiccating conditions. Six genes encoding potential light sensors were identified in strain TTB310. Two genes encode for bacteriophytochromes, while the four remaining genes encode for putative blue light receptors. We determined the spectral and photochemical properties of the two recombinant bacteriophytochromes RtBphP1 and RtBphP2. In both cases, they act as sensitive red light detectors. Cyst divisions and a complete cyst-rod-cyst cycle are the main processes in darkness, whereas rod divisions predominate in red or far-red light. Mutant phenotypes caused by the inactivation of genes encoding bacteriophytochromes or heme oxygenase clearly show that both bacteriophytochromes are involved in regulating the rod-rod division. This process could favor rapid rod divisions at sunrise, after dew formation but before the progressive onset of desiccation. Our study provides the first evidence of a light-based strategy evolved in a non-photosynthetic bacterium to exploit scarse water in a desert environment.

Ottowia flava sp. nov., isolated from fish intestines.

A novel Gram-negative bacterium, non-motile and short rod-shaped, designated strain GY511T, was isolated from the intestines of fish collected from Maowei Sea, China. Growth occurred at pH 6.0-9.0 (optimum 7.0), 4-37 °C (optimum 28 °C) and at 0-2.5% (w/v) NaCl (optimum 1.0%). The result of 16S rRNA gene sequence analysis showed that strain GY511T is closely related to O. oryzae NBRC 113109T (97.6%), O. konkukae DSM 105395T (97.4%), Ottowia beijingensis CGMCC 1.12324T (95.9%), Ottowia pentelensis DSM 21699T (95.2%) and Ottowia thiooxydans DSM 14619T (95.0%). The DNA-DNA hybridization values of strain GY511T with O. oryzae NBRC 113109T and O. konkukae DSM 105395T were 35.4 ± 3.1% and 26.3 ± 1.8%, respectively. The major fatty acids (> 10%) were identified as summed feature 3 (C16:1ω7c and/or C16:1ω6c), C16:0 and summed feature 8 (C18:1ω7c and/or C18:1ω6c) and the major respiratory quinone was ubiquinone-8 (Q-8). The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmethylethanolamine, two unidentified aminolipids and an unidentified phospholipid. The G+C content of the genomic DNA was 62.9 mol%. Thiosulfate could be utilized as co-substrate for aerobic growth and was oxidised to sulfate. On the basis of phenotypic, chemotaxonomic and molecular data, strain GY511T is considered to represent a novel species of the genus Ottowia, for which the name Ottowia flava sp. nov. is proposed. The type strain is GY511T (= NBRC 113500T = DSM 107425T = CGMCC 1.13650T).

A Nodulation-Proficient Nonrhizobial Inhabitant of Pueraria phaseoloides.

Pueraria phaseoloides is a legume cover crop, found chiefly in the wet zone of Sri Lanka. Nitrogen fixation is performed by nodular inhabitants of this cover crop, comparable to the nodule-dwelling bacteria of most other legume plants. We isolated a bacterium (Sub1) from Pueraria phaseoloides, of coccobacillus cell shape, that showed nodulation, when assessed by hydroponics, showing nodules as early as 3 weeks after reinfection. When a nifH fragment from the genome of this bacterium was amplified using a pair of nifH primers, it yielded an amplicon of 360 bp that, when sequenced, helped us identify the bacterium, as belonging to a species of Pseudacidovorax intermedius, at 99% sequence identity. When we constructed a phylogenetic tree with neighboring sequences, we encountered nifH sequences of Pseudacidovorax, forming a monophyletic cluster, which too contained a single Azospirillum species. The genus Pseudacidovorax is a bacterium that, so far, has not been associated with legume nodules. Sub1 secreted a pair of enzymes to the extracellular medium to degrade cellulose and milk proteins. The Sub1 bacterium showed biofilm formation and secreted into the extracellular medium, indole acetic acid. Sub1 also showed a "bulls eye" swarming pattern for the chemoattractant proline, while showing no significant chemotaxis movement, for naringenin, quercetin, and glutamate. Sub1 too possesses the basic genetic foundation (nifH and nifD) to produce a molybdenum-dependent nitrogenase enzyme. We finally show that this rare nonrhizobial bacterium is able to impact, positively, nodulation and shoot length of Pueraria plants, demonstrating that this beta-proteobacterium can abet the biological vigor of this legume cover crop.

Dominance of the genus Polaromonas in the microbial ecology of an Intermittently Aerated Sequencing Batch Reactor (IASBR) treating dairy processing wastewater under varying aeration rates.

In this Research Communication we investigate potential correlations between key bacterial groups and nutrient removal efficiency in an Intermittently Aerated Sequencing Batch Reactor (IASBR) treating synthetic dairy processing wastewater. Reactor aeration rates of 0·6 and 0·4 litre per minute (LPM) were applied to an 8 l laboratory scale system and the relative impacts on IASBR microbial community structure and orthophosphate (PO4-P) and ammonium (NH4-N) removal efficiencies compared. Aeration at 0·6 LPM over several sludge retention times (SRTs) resulted in approximately 92% removal efficiencies for both PO4-P and NH4-N. Biomass samples subjected to next-generation sequencing (NGS), 16S rRNA profiling revealed a concomitant enrichment of Polaromonas under 0·6 LPM conditions, up to ~50% relative abundance within the reactor biomass. The subsequent shift in reactor aeration to 0·4 LPM, over a period of 3 SRTs, resulted in markedly reduced nutrient removal efficiencies for PO4-P (50%) and NH4-N (45%). An 85·7% reduction in the genus level relative abundance of Polaromonas was observed under 0·4 LPM aeration conditions over the same period.

Interaction between the microbiome and TP53 in human lung cancer.

BACKGROUND: Lung cancer is the leading cancer diagnosis worldwide and the number one cause of cancer deaths. Exposure to cigarette smoke, the primary risk factor in lung cancer, reduces epithelial barrier integrity and increases susceptibility to infections. Herein, we hypothesize that somatic mutations together with cigarette smoke generate a dysbiotic microbiota that is associated with lung carcinogenesis. Using lung tissue from 33 controls and 143 cancer cases, we conduct 16S ribosomal RNA (rRNA) bacterial gene sequencing, with RNA-sequencing data from lung cancer cases in The Cancer Genome Atlas serving as the validation cohort. RESULTS: Overall, we demonstrate a lower alpha diversity in normal lung as compared to non-tumor adjacent or tumor tissue. In squamous cell carcinoma specifically, a separate group of taxa are identified, in which Acidovorax is enriched in smokers. Acidovorax temporans is identified within tumor sections by fluorescent in situ hybridization and confirmed by two separate 16S rRNA strategies. Further, these taxa, including Acidovorax, exhibit higher abundance among the subset of squamous cell carcinoma cases with TP53 mutations, an association not seen in adenocarcinomas. CONCLUSIONS: The results of this comprehensive study show both microbiome-gene and microbiome-exposure interactions in squamous cell carcinoma lung cancer tissue. Specifically, tumors harboring TP53 mutations, which can impair epithelial function, have a unique bacterial consortium that is higher in relative abundance in smoking-associated tumors of this type. Given the significant need for clinical diagnostic tools in lung cancer, this study may provide novel biomarkers for early detection.

Polyphasic characterization of four soil-derived phenanthrene-degrading Acidovorax strains and proposal of Acidovorax carolinensis sp. nov.

Four bacterial strains identified as members of the Acidovorax genus were isolated from two geographically distinct but similarly contaminated soils in North Carolina, USA, characterized, and their genomes sequenced. Their 16S rRNA genes were highly similar to those previously recovered during stable-isotope probing (SIP) of one of the soils with the polycyclic aromatic hydrocarbon (PAH) phenanthrene. Heterotrophic growth of all strains occurred with a number of organic acids, as well as phenanthrene, but no other tested PAHs. Optimal growth occurred aerobically under mesophilic temperature, neutral pH, and low salinity conditions. Predominant fatty acids were C16:1ω7c/C16:1ω6c, C16:0, and C18:1ω7c, and were consistent with the genus. Genomic G+C contents ranged from 63.6 to 64.2%. A combination of whole genome comparisons and physiological analyses indicated that these four strains likely represent a single species within the Acidovorax genus. Chromosomal genes for phenanthrene degradation to phthalate were nearly identical to highly conserved regions in phenanthrene-degrading Delftia, Burkholderia, Alcaligenes, and Massilia species in regions flanked by transposable or extrachromosomal elements. The lower degradation pathway for phenanthrene metabolism was inferred by comparisons to described genes and proteins. The novel species Acidovorax carolinensis sp. nov. is proposed, comprising the four strains described in this study with strain NA3T as the type strain (=LMG 30136, =DSM 105008).

An Aberrant Microbiota is not Strongly Associated with Incidental Colonic Diverticulosis.

Colonic diverticula are protrusions of the mucosa through weak areas of the colonic musculature. The etiology of diverticulosis is poorly understood, but could be related to gut bacteria. Using mucosal biopsies from the sigmoid colon of 226 subjects with and 309 subjects without diverticula during first-time screening colonoscopy, we assessed whether individuals with incidental colonic diverticulosis have alternations in the adherent bacterial communities in the sigmoid colon. We found little evidence of substantial associations between the microbial community and diverticulosis among cases and controls. Comparisons of bacterial abundances across all taxonomic levels showed differences for phylum Proteobacteria (p = 0.038) and family Comamonadaceae (p = 0.035). The r-squared values measuring the strength of these associations were very weak, however, with values ~2%. There was a similarly small association between the abundance of each taxa and total diverticula counts. Cases with proximal only diverticula and distal only diverticula likewise showed little difference in overall microbiota profiles. This large study suggests little association between diverticula and the mucosal microbiota overall, or by diverticula number and location. We conclude that the mucosal adherent microbiota community composition is unlikely to play a substantial role in development of diverticulosis.

Association Between Loss of Type IV Pilus Synthesis Ability and Phenotypic Variation in the Cucurbit Pathogenic Bacterium Acidovorax citrulli.

Acidovorax citrulli is the causal agent of bacterial fruit blotch of cucurbits. We have shown that functional type IV pili (T4P) are required for full virulence of this bacterium. To identify A. citrulli genes required for T4P activity, we screened a library of about 10,000 transposon mutants of A. citrulli M6 for altered T4P-mediated twitching motility. This screen led to the identification of 50 mutants impaired in twitching ability due to transposon insertions into 20 different genes. Representative mutants with disruptions in these genes were further characterized. All mutants were compromised in their virulence in seed transmission and stem inoculation assays and had reduced biofilm formation ability relative to wild-type M6. When grown on nutrient agar, most mutants produced colonies with a translucent and fuzzy appearance, in contrast to the opaque and smooth appearance of wild-type colonies. The colony morphology of these mutants was identical to that of previously reported phenotypic variants of strain M6. The exceptions were M6 mutants disrupted in genes tonB, pilT, pilW, and pilX that exhibited typical wild-type colony morphology, although lacking twitching haloes surrounding the colony. Transmission electron microscopy revealed that most mutants lacked the ability to produce T4P. The exceptions were mutants with disruptions in tonB, pilT, pilW, and pilX genes that were shown to produce these appendages. These findings support the idea that colony phenotypic variation in A. citrulli is determined by the lack of ability to synthesize T4P but not by lack of T4P functionality.

Rhodoferax koreense sp. nov, an obligately aerobic bacterium within the family Comamonadaceae, and emended description of the genus Rhodoferax.

Gram-staining-negative, uniflagellated, rod-shaped, designated as DCY110T, was isolated from sludge located in Gangwon province, Republic of Korea. The phylogenetic tree of 16S rRNA gene sequence showed that the strain DCY110T belonged to the genus Rhodoferax with a close similarity to Rhodoferax saidenbachensis DSM 22694T (97.7%), Rhodoferax antarcticus DSM 24876T (97.5%), Rhodoferax ferrireducens DSM 15236T (97.3%), and Rhodoferax fermentans JCM 7819T (96.7%). The predominant isoprenoid quinine was ubiquinone (Q-8). DNA G + C content was 62.8 mol%. The major polar lipids were phosphatidylethanolamine and two unidentified phospholipids. The major fatty acids (> 10%) were C12:0, C16:0, summed feature 3 (which comprised C16:1 ω7c and/or C16:1 ω6c). The DNA-DNA relatedness values between the strain DCY110T and the closely related relatives used in this study were lower than 70%. Based on the following polyphasic analysis, the strain DCY110T is considered as a novel species of the genus Rhodoferax, for which the name Rhodoferax koreense sp. nov. is proposed. The type strain is DCY-110T (= KCTC 52288T = JCM 31441T).

Acidovorax lacteus sp. nov., isolated from a culture of a bloom-forming cyanobacterium (Microcystis sp.).

A novel Gram-negative, rod-shaped and motile bacterial strain, designated strain M36T, was isolated from a culture of a bloom-forming cyanobacterium, Microcystis sp., collected from a eutrophic lake in Korea. Its taxonomic position was investigated by using a polyphasic taxonomic approach. The isolate was found to grow aerobically at 15-42 °C (optimum 25 °C), pH 7.0-11.0 (optimum pH 8.0) and in the presence of 0-1.0% (w/v) NaCl (optimum 0% NaCl) on R2A medium. The phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain M36T is closely related to Acidovorax anthurii DSM 16745T (98.1%), Acidovorax konjaci DSM 7481T (97.7%) and Acidovorax avenae DSM 7227T (97.0%) and also formed a clear phylogenetic lineage with other Acidovorax species. DNA-DNA relatedness between strain M36T and the closely related species of the genus Acidovorax was <30%. The major fatty acid components identified included summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0 and summed feature 8 (C18:0 ω7c and/or C18:0 ω6c). The DNA G+C content of strain M36T was determined to be 66.8 mol%. Based on above polyphasic evidence, strain M36T is concluded to represent a new species of genus Acidovorax, for which the name Acidovorax lacteus sp. nov. is proposed. The type strain is M36T (=KCTC 52220T = JCM 31890T).

A Novel Quorum-Quenching N-Acylhomoserine Lactone Acylase from Acidovorax sp. Strain MR-S7 Mediates Antibiotic Resistance.

N-Acylhomoserine lactone acylase (AHL acylase) is a well-known enzyme responsible for disrupting cell-cell communication (quorum sensing) in bacteria. Here, we isolated and characterized a novel and unique AHL acylase (designated MacQ) from a multidrug-resistant bacterium, Acidovorax sp. strain MR-S7. The purified MacQ protein heterologously expressed in Escherichia coli degraded a wide variety of AHLs, ranging from C6 to C14 side chains with or without 3-oxo substitutions. We also observed that AHL-mediated virulence factor production in a plant pathogen, Pectobacterium carotovorum, was dramatically attenuated by coculture with MacQ-overexpressing Escherichia coli, whereas E. coli with an empty vector was unable to quench the pathogenicity, which strongly indicates that MacQ can act in vivo as a quorum-quenching enzyme and interfere with the quorum-sensing system in the pathogen. In addition, this enzyme was found to be capable of degrading a wide spectrum of ß-lactams (penicillin G, ampicillin, amoxicillin, carbenicillin, cephalexin, and cefadroxil) by deacylation, clearly indicating that MacQ is a bifunctional enzyme that confers both quorum quenching and antibiotic resistance on strain MR-S7. MacQ has relatively low amino acid sequence identity to any of the known acylases (<39%) and has among the broadest substrate range. Our findings provide the possibility that AHL acylase genes can be an alternative source of antibiotic resistance genes posing a threat to human health if they migrate and transfer to pathogenic bacteria.IMPORTANCEN-Acylhomoserine lactones (AHLs) are well-known signal molecules for bacterial cell-cell communication (quorum sensing), and AHL acylase, which is able to degrade AHLs, has been recognized as a major target for quorum-sensing interference (quorum quenching) in pathogens. In this work, we succeeded in isolating a novel AHL acylase (MacQ) from a multidrug-resistant bacterium and demonstrated that the MacQ enzyme could confer multidrug resistance as well as quorum quenching on the host organism. Indeed, the purified MacQ protein was found to be bifunctional and capable of degrading not only various AHL derivatives but also multiple ß-lactam antibiotics by deacylation activities. Although quorum quenching and antibiotic resistance have been recognized to be distinct biological functions, our findings clearly link the two functions by discovering the novel bifunctional enzyme and further providing the possibility that a hitherto-overlooked antibiotic resistance mechanism mediated by the quorum-quenching enzyme may exist in natural environments and perhaps in clinical settings.