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The largest living rodent, capybara, can efficiently depolymerize and utilize lignocellulosic biomass through microbial symbiotic mechanisms yet elusive. Herein, we elucidate the microbial community composition, enzymatic systems and metabolic pathways involved in the conversion of dietary fibers into short-chain fatty acids, a main energy source for the host. In this microbiota, the unconventional enzymatic machinery from Fibrobacteres seems to drive cellulose degradation, whereas a diverse set of carbohydrate-active enzymes from Bacteroidetes, organized in polysaccharide utilization loci, are accounted to tackle complex hemicelluloses typically found in gramineous and aquatic plants. Exploring the genetic potential of this community, we discover a glycoside hydrolase family of β-galactosidases (named as GH173), and a carbohydrate-binding module family (named as CBM89) involved in xylan binding that establishes an unprecedented three-dimensional fold among associated modules to carbohydrate-active enzymes. Together, these results demonstrate how the capybara gut microbiota orchestrates the depolymerization and utilization of plant fibers, representing an untapped reservoir of enzymatic mechanisms to overcome the lignocellulose recalcitrance, a central challenge toward a sustainable and bio-based economy. ispartof: NATURE COMMUNICATIONS vol:13 issue:1 ispartof: location:England status: published

The sequence of the DNA contains coding and non-coding regions. The role of the non-coding regions is not known and is hypothesized to maintain the structure of the DNA. This study aimed to investigate the structure of the non-coding sequences in honey bees utilizing bioinformatics. The non-coding sequences of the mtDNA of three honey bee species Apis dorosata, Apis florea, Apis cerana, and ten subspecies of Apis mellifera were investigated. Different techniques were utilized to explore the non-coding regions of these bees including sequence analysis, phylogenetic relationships, enzymatic digestion, and statistical tests. Variations in size and sequences of nucleotides were detected in the studied species and subspecies, but with the same nucleotide abundance (i.e. nucleotides A were more than T and nucleotides G were less than C). The phylogenetic tree based on the non-coding regions was partially similar to the known phylogenetic relationships between these bees. The enzymatic digestion using four restriction enzymes confirmed the results of the phylogenetic relationships. The statistical analysis based on numerical codes for nucleotides showed the absence of significant variations between the studied bees in their sequences in a similar way to results of neutrality tests. This study suggests that the non-coding regions have the same functional role in all the studied bees regardless of the number of nucleotides, and not just to maintain the structure of the DNA. This is approximately the first study to shade lights on the non-coding regions of the mtDNA of honey bees.

Whereas most work to understand impacts of humans on biodiversity on coastal areas has focused on large, conspicuous organisms, we highlight effects of tourist access on the diversity of microscopic marine animals (meiofauna). We used a DNA metabarcoding approach with an iterative and phylogeny-based approach for the taxonomic assignment of meiofauna and relate diversity patterns to the numbers of tourists accessing sandy beaches on an otherwise un-impacted island National Park. Tourist frequentation, independently of differences in sediment granulometry, beach length, and other potential confounding factors, affected meiofaunal diversity in the shallow “swash” zone right at the mean water mark; the impacts declined with water depth (up to 2 m). The indicated negative effect on meiofauna may have a consequence on all the biota including the higher trophic levels. Thus, we claim that it is important to consider restricting access to beaches in touristic areas, in order to preserve biodiversity., Martínez et al. use DNA metabarcoding and a phylogeny-based approach to demonstrate the effects of tourist access on meiofauna diversity of beaches in Asinara National Park. Their results show that tourist frequentation decreases meiofaunal diversity at the shallow “swash” zone, and can be used to inform tourist access and management of beaches.

Sulfate reduction is an important biogeochemical process in the ecosphere; however, the major taxa of sulfate reducers have not been fully identified. Here, we used epicPCR (Emulsion, Paired Isolation, and Concatenation PCR) technology to identify the phylogeny of sulfate-reducing prokaryotes (SRP) in sediments from Tibetan Plateau saline lakes. A total of 12,519 OTUs and 883 SRP-OTUs were detected in ten lakes by sequencing of 16S rRNA gene PCR amplicons and epicPCR products of fused 16S rRNA plus dsrB gene, respectively, with Proteobacteria, Firmicutes, and Bacteroidetes being the dominant phyla in both datasets. The 120 highly abundant SRP-OTUs (> 1% in at least one sample) were affiliated with 17 described phyla, only 7 of which are widely recognized as SRP phyla. The majority of OTUs from both the whole microbial communities and the SRPs were not detected in more than one specific lake, suggesting high levels of endemism. The α-diversity of the entire microbial community and SRP sub-community showed significant positive correlations. The pH value and mean water temperature of the month prior to sampling were the environmental determinants for the whole microbial community, while the mean water temperature and total nitrogen were the major environmental drivers for the SRP sub-community. This study revealed there are still many undocumented SRP in Tibetan saline lakes, many of which could be endemic and adapted to specific environmental conditions. Electronic supplementary material The online version of this article (10.1186/s40168-019-0688-4) contains supplementary material, which is available to authorized users.

Introduction: There are two methods of reverse transcription polymerase chain reaction (RT–PCR) that have been the common methods to detect influenza infections: conventional and real-time RT–PCR. From December 2017 to March 2018, several missed diagnoses of influenza A(H1)pdm09 using real-time RT–PCR were reported in northern Viet Nam. This study investigated how these missed detections occurred to determine their effect on the surveillance of influenza. Methods: The haemagglutinin (HA) segments of A(H1N1)pdm09 from both real-time RT-PCR positive and negative samples were isolated and sequenced. The primer and probe sets in the HA gene were checked for mismatches, and phylogenetic analyses were performed to determine the molecular epidemiology of these viruses. Results: There were 86 positive influenza A samples; 32 were A(H1)pdm09 positive by conventional RT–PCR but were negative by real-time RT–PCR. Sequencing was conducted on 23 influenza (H1N1)pdm09 isolates that were recovered from positive samples. Eight of these were negative for A(H1)pdm09 by real-time RT–PCR. There were two different mismatches in the probe target sites of the HA gene sequences of all isolates (n = 23) with additional mismatches only at position 7 (template binding site) identified for all eight negative real-time RT–PCR isolates. The prime target sites had no mismatches. Phylogenetic analysis of the HA gene showed that both the positive and negative real-time RT–PCR isolates were grouped in clade 6B.1; however, the real-time RT–PCR negative viruses were located in a subgroup that referred to substitution I295V. Conclusion: Constant monitoring of genetic changes in the circulating influenza A(H1N1)pdm09 viruses is important for maintaining the sensitivity of molecular detection assays.

The gut microbiome plays an important role in a host’s development and adaption to its dietary niche. In this study, a group of bamboo-feeding insects are used to explore the potential role of the gut microbiota in the convergent adaptation to extreme diet specialization. Specifically, using a 16S rRNA marker and an Illumina sequencing platform, we profiled the microbial communities of 76 gut samples collected from nine bamboo-feeding insects, including both hemimetabolous (Orthoptera and Hemiptera) and holometabolous (Coleoptera and Lepidoptera) species, which are specialized in three distinct dietary niches: bamboo leaf, shoot, and sap. The gut microbiota of these insects were dominated by Proteobacteria, Firmicutes, and Bacteroidetes and were clustered into solid (leaf and shoot) and liquid (sap) dietary niches. The gut bacterial communities of insects feeding on solid diet overlapped significantly, even though these insects belong to phylogenetically distant lineages representing different orders. In addition, the presence of cellulolytic bacterial communities within the gut microbiota allows bamboo-feeding insects to adapt to a highly specialized, fiber-rich diet. Although both phylogeny and diet can impact the structure and composition of gut microbiomes, phylogeny is the primary driving force underlying the convergent adaptation to a highly specialized diet, especially when the related insect species harbor similar gut microbiomes and share the same dietary niche over evolutionary timescales. These combined findings lay the foundation for future research on how convergent feeding strategies impact the interplays between hosts and their gut microbiomes and how the gut microbiota may facilitate convergent evolution in phylogenetically distant species in adaptation to the shared diet.

The Congo Basin region is believed to be the site of the cross-species transmission event that yielded HIV-1 group M (HIV-1M). It is thus likely that the virus has been present and evolving in the region since that cross-species transmission. As HIV-1M was only discovered in the early 1980s, our directly observed record of the epidemic is largely limited to the past four decades. Nevertheless, by exploiting the genetic relatedness of contemporary HIV-1M sequences, phylogenetic methods provide a powerful framework for investigating simultaneously the evolutionary and epidemiologic history of the virus. Such an approach has been taken to find that the currently classified HIV-1 M subtypes and Circulating Recombinant Forms (CRFs) do not give a complete view of HIV-1 diversity. In addition, the currently identified major HIV-1M subtypes were likely genetically predisposed to becoming a major component of the present epidemic, even before the events that resulted in the global epidemic. Further efforts have identified statistically significant hot- and cold-spots of HIV-1M subtypes sequence inheritance in genomic regions of recombinant forms. In this review we provide ours and others recent findings on the emergence and spread of HIV-1M variants in the region, which have provided insights into the early evolution of this virus.

Europe is a rich combination of diversities, cultures, and populations. Roma is the largest ethnic minority of Europe, accounting for an estimated >10 million citizens, although no official census is available. In this thesis, sex-biased demographic processes in Roma people are introduced. The comparison of mitochondrial DNA and Y-chromosome sequences show that the Roma maternal genetic pool carries higher lineage diversity, both in the South Asian and European fractions. On the contrary, a single South Asian lineage dominates their paternal genetic landscape. The results of this project suggest that socio-cultural factors influenced the emergence of these patterns at global and local scales in the Roma. Uniparental genomes are especially suitable for kinship analyses, mixed DNA cases and geographical ancestry in forensic identifications. In this thesis, we analyze the uniparental sequences of the resident population in Catalonia, to analyze the potential of this data for forensic genetics. We proved the robustness of this type of data in unequivocal identifications and found that they provide higher resolution than previous markers. Lastly, we optimize and apply a target enrichment technique to capture the regions of the Y chromosome that are suitable for population genetics studies. As R1b-DF27 is the most frequent haplogroup in the Iberian Peninsula and has an interesting and debated history, we use the capture technique to refine its phylogeny and phylogeography. Europa es una rica combinación de diversidades, culturas y poblaciones. Los Roma son la minoría étnica más grande de Europa; se estima que su población supera los 10 millones de ciudadanos. Sin embargo, no existe un censo oficial disponible. En esta tesis introducimos los procesos demográficos de los Roma, que presentan un notable sesgo por sexo genético. La comparación de secuencias de ADN mitocondrial y del cromosoma Y muestran que el acervo genético materno de los Roma tiene una alta diversidad de linajes, tanto en la fracción de origen surasiático como en la europea. El panorama genético paterno, al contrario, está dominado por una elevada frecuencia de un solo linaje surasiático. Los resultados de este proyecto sugieren que factores socioculturales ligados al sexo genético han influido en la emergencia de estos patrones sesgados en los Roma a nivel local y global. Los genomas uniparentales son especialmente útiles para realizar análisis de parentesco e identificación forense en casos de mezclas de ADN, así como para inferir ascendencia geográfica. En esta tesis analizamos secuencias uniparentales de la población residente en Catalunya, para estudiar el potencial de este tipo de datos en genética forense. Hemos comprobado la robustez de las secuencias en identificaciones inequívocas, y observamos que otorgan una mayor resolución que los marcadores usados tradicionalmente. Durante la última fase esta tesis, hemos optimizado una técnica para capturar específicamente las regiones del cromosoma Y que se usan para estudios de genética de poblaciones. Dado que R1b-DF27 es el haplogrupo más frecuente en la Península Ibérica, y tiene una interesante y debatida historia, hemos utilizado nuestro protocolo de captura para refinar su filogenia y filogeografía.

Salmonella enterica ser. Typhimurium monophasic variant 4,[5],12:i:- has been associated with food-borne epidemics worldwide and swine appeared to be the main reservoir in most of the countries of isolation. However, the monomorphic nature of this serovar has, so far, hindered identification of the source due to expansion of clonal lineages in multiple hosts and food producing systems. Since geographically structured genetic signals can shape bacterial populations, identification of biogeographical markers in S. 1,4,[5],12:i:- genomes can contribute to improving source attribution. In this study, the phylogeographical structure of 148 geographically and temporally related Italian S. 1,4,[5],12:i:- has been investigated. The Italian isolates belong to a large population of clonal S. Typhimurium/1,4,[5],12:i:- isolates collected worldwide in two decades showing up to 2.5% of allele differences. Phylogenetic reconstruction revealed that isolates from the same geographical origin form highly supported monophyletic groups, suggesting discrete geographical segregation. These monophyletic groups are characterized by the gene content of a large sopE-containing prophage. Within this prophage, genome-wide comparison identified several genes overrepresented in strains of Italian origin. This suggests that certain lineages may be characterized by the acquisition of specific accessory genetic markers useful for improving identification of the source in ongoing epidemics.

Three species currently addressed to Protohydnum (Auriculariales) are studied with morphological and DNA methods. The genus Protohydnum is retained for the type species only, P. cartilagineum, recently re-collected in Brazil. The European species, P. piceicola, is not congeneric with P. cartilagineum and, therefore, placed in its own genus, Hyalodon, gen. nov. Another Hyalodon species, H. antui, is described from East Asia. The third member of Protohydnum sensu lato, P. sclerodontium from South-East Asia, is transferred to Elmerina.

The presence of extended-spectrum β-lactamase (ESBL) or plasmid-mediated AmpC β-lactamase (pAmpC)-producing Escherichia coli (ESBL/pAmpC-EC) in livestock is a public health risk given the likelihood of their transmission to humans via the food chain. We conducted whole genome sequencing on 100 ESBL/pAmpC-EC isolated from the broiler production to explore their resistance and virulence gene repertoire, characterise their plasmids and identify transmission events derived from their phylogeny. Sequenced isolates carried resistance genes to four antimicrobial classes in addition to cephalosporins. Virulence gene analysis assigned the majority of ESBL/pAmpC-EC to defined pathotypes. In the complex genetic background of ESBL/pAmpC-EC, clusters of closely related isolates from various production stages were identified and indicated clonal transmission. Phylogenetic comparison with publicly available genomes suggested that previously uncommon ESBL/pAmpC-EC lineages could emerge in poultry, while others might contribute to the maintenance and dissemination of ESBL/pAmpC genes in broilers. The majority of isolates from diverse E. coli lineages shared four dominant plasmids (IncK2, IncI1, IncX3 and IncFIB/FII) with identical ESBL/pAmpC gene insertion sites. These plasmids have been previously reported in diverse hosts, including humans. Our findings underline the importance of specific plasmid groups in the dissemination of cephalosporin resistance genes within the broiler industry and across different reservoirs.

During fungal surveys between 2012 and 2014 in pine-dominated forests of the western Himalayas in Pakistan, several collections of Pseudosperma (Agaricales, Inocybaceae) were made. These were documented, based on morphological and molecular data. During this work, three new species came to light, which are here formally described as Pseudosperma brunneoumbonatum, P. pinophilum and P. triacicularis. These species belong in the genus Pseudosperma fideMatheny et al. (2019) = Pseudosperma clade fideMatheny (2005) = Inocybe sect. Rimosae s.s. fideLarsson et al. (2009). Macro- and micro-morphological descriptions, illustrations and molecular phylogenetic reconstructions of the studied taxa are provided. The new species are differentiated from their close relatives by basidiospore size and colouration of basidiomata. Molecular phylogenetic relationships are inferred using ITS (ITS1–5.8S–ITS2), nrLSU and mtSSU sequence data. All three newly-described taxa likely share an ectomycorrhizal association with trees in the genus Pinus. In addition, five names are recombined in Inosperma, Mallocybe and Pseudosperma. These are Inosperma vinaceobrunneum, Mallocybe erratum, Pseudosperma alboflavellum, Pseudosperma friabile and Pseudosperma neglectum.

Place: Hoboken Publisher: Wiley WOS:000601909000001; Although many studies have investigated the spatial scaling of microbial communities living in surface soils, very little is known about the patterns within deeper strata, nor is the mechanism behind them. Here, we systematically assessed spatial scaling of prokaryotic biodiversity within three different strata (Upper: 0-20 cm, Middle: 20-40 cm, and Substratum: 40-100 cm) in a typical grassland by examining both distance-decay (DDRs) and species-area relationships (SARs), taxonomically and phylogenetically, as well as community assembly processes. Each layer exhibited significant biogeographic patterns in both DDR and SAR (p \textless .05), with taxonomic turnover rates higher than phylogenetic ones. Specifically, the spatial turnover rates, beta and z values, respectively, ranged from 0.016 +/- 0.005 to 0.023 +/- 0.005 and 0.065 +/- 0.002 to 0.077 +/- 0.004 across soil strata, and both increased with depth. Moreover, the prokaryotic community in grassland soils assembled mainly according to deterministic rather than stochastic mechanisms. By using normalized stochasticity ratio (NST) based on null model, the relative importance of deterministic ratios increased from 48.0 to 63.3% from Upper to Substratum, meanwhile a phylogenetic based method revealed average beta NTI also increased with depth, from -5.29 to 19.5. Using variation partitioning and distance approaches, both geographic distance and soil properties were found to strongly affect biodiversity structure, the proportions increasing with depth, but spatial distance was always the main underlying factor. These indicated increasingly deterministic proportions in accelerating turnover rates for spatial assembly of prokaryotic biodiversity. Our study provided new insights on biogeography in different strata, revealing importance of assembly patterns and mechanisms of prokaryote communities in below-surface soils.

Reproductive isolation is an important component of species differentiation. The plastid accD gene coding for the acetyl-CoA carboxylase subunit and the nuclear bccp gene coding for the biotin carboxyl carrier protein were identified as candidate genes governing nuclear-cytoplasmic incompatibility in peas. We examined the allelic diversity in a set of 195 geographically diverse samples of both cultivated (Pisum sativum, P. abyssinicum) and wild (P. fulvum and P. elatius) peas. Based on deduced protein sequences, we identified 34 accD and 31 bccp alleles that are partially geographically and genetically structured. The accD is highly variable due to insertions of tandem repeats. P. fulvum and P. abyssinicum have unique alleles and combinations of both genes. On the other hand, partial overlap was observed between P. sativum and P. elatius. Mapping of protein sequence polymorphisms to 3D structures revealed that most of the repeat and indel polymorphisms map to sequence regions that could not be modeled, consistent with this part of the protein being less constrained by requirements for precise folding than the enzymatically active domains. The results of this study are important not only from an evolutionary point of view but are also relevant for pea breeding when using more distant wild relatives.

In this study, molecular (ribosomal sequence data), morphological and cross-hybridization properties were used to identify a newSteinernemasp. from Florida, USA. Molecular and morphological data provided evidence for placing the novel species into Clade V, or the ‘glaseri-group’ ofSteinernemaspp. Within this clade, analysis of sequence data of the rDNA genes, 28S and internal transcribed spacer (ITS), depicted the novel species as a distinctive entity and closely related toS. glaseriandS. cubanum.Additionally, cross-hybridization assays showed that the new species is unable to interbreed with either of the latter two species, reinforcing its uniqueness from a biological species concept standpoint. Key morphological diagnostic characters forS. khuongin. sp. include the mean morphometric features of the third-stage infective juveniles: total body length (average: 1066 μm), tail length (average: 65 μm), location of the excretory pore (average: 80.5 μm) and the values ofc(average: 16.4),D% (average: 60.5),E% (average: 126) andH% (average: 46.6). Additionally, males can be differentiated fromS. glaseriandS. cubanumby the values of several ratios:D% (average: 68),E% (average: 323) and SW% (average: 120). The natural distribution of this species in Florida encompasses both natural areas and citrus groves, primarily in shallow groundwater ecoregions designated as ‘flatwoods’. The morphological, molecular, phylogenetic and ecological data associated with this nematode support its identity as a new species in theS. glaseri-group.

Stem-pitting (SP) is the main type of citrus tristeza virus (CTV) that causes severe damage to citrus trees, especially those of sweet orange, in Hunan province, China. Understanding the local CTV population structure should provide clues for effective mild strain cross-protection (MSCP) of the SP strain of CTV. In this study, markers for the p23 gene, multiple molecular markers (MMMs), and sequence analysis of the three silencing suppressor genes (p20, p23 and p25) were employed to analyze the genetic diversity and genotype composition of the CTV population based on 51 CTV-positive samples collected from 14 citrus orchards scattered around six major citrus-growing areas of Hunan. The results indicated that the CTV population structure was extremely complex and that infection was highly mixed. In total, p23 gene markers resulted in six profiles, and MMMs demonstrated 25 profiles. The severe VT and T3 types appeared to be predominantly associated with SP, while the mild T30 and RB types were related to asymptomatic samples. Based on phylogenetic analysis of the amino acid sequences of p20, p23 and p25, 19 representative CTV samples were classified into seven recently established CTV groups and a potentially novel one. A high level of genetic diversity, as well as potential recombination, was revealed among different CTV isolates. Five pure SP severe and two pure mild strains were identified by genotype composition analysis. Taken together, the results update the genetic diversity of CTV in Hunan with the detection of one possible novel strain, and this information might be applicable for the selection of appropriate mild CTV strains for controlling citrus SP disease through cross-protection.

We present fastbaps, a fast solution to the genetic clustering problem. Fastbaps rapidly identifies an approximate fit to a Dirichlet Process Mixture model (DPM) for clustering multilocus genotype data. Our efficient model-based clustering approach is able to cluster datasets 10-100 times larger than the existing model-based methods, which we demonstrate by analysing an alignment of over 110,000 sequences of HIV-1 pol genes. We also provide a method for rapidly partitioning an existing hierarchy in order to maximise the DPM model marginal likelihood, allowing us to split phylogenetic trees into clades and subclades using a population genomic model. Extensive tests on simulated data as well as a diverse set of real bacterial and viral datasets show that fastbaps provides comparable or improved solutions to previous model-based methods, while generally being significantly faster. The method is made freely available under an open source MIT licence as an easy to use R package athttps://github.com/gtonkinhill/fastbaps.

Identification of Shigella spp., Escherichia coli, and enteroinvasive E. coli (EIEC) is challenging because of their close relatedness. Distinction is vital, as infections with Shigella spp., Identification of Shigella spp., Escherichia coli, and enteroinvasive E. coli (EIEC) is challenging because of their close relatedness. Distinction is vital, as infections with Shigella spp. are under surveillance of health authorities, in contrast to EIEC infections. In this study, a culture-dependent identification algorithm and a molecular identification algorithm were evaluated. Discrepancies between the two algorithms and original identification were assessed using whole-genome sequencing (WGS). After discrepancy analysis with the molecular algorithm, 100% of the evaluated isolates were identified in concordance with the original identification. However, the resolution for certain serotypes was lower than that of previously described methods and lower than that of the culture-dependent algorithm. Although the resolution of the culture-dependent algorithm is high, 100% of noninvasive E. coli, Shigella sonnei, and Shigella dysenteriae, 93% of Shigella boydii and EIEC, and 85% of Shigella flexneri isolates were identified in concordance with the original identification. Discrepancy analysis using WGS was able to confirm one of the used algorithms in four discrepant results. However, it failed to clarify three other discrepant results, as it added yet another identification. Both proposed algorithms performed well for the identification of Shigella spp. and EIEC isolates and are applicable in low-resource settings, in contrast to previously described methods that require WGS for daily diagnostics. Evaluation of the algorithms showed that both algorithms are capable of identifying Shigella species and EIEC isolates. The molecular algorithm is more applicable in clinical diagnostics for fast and accurate screening, while the culture-dependent algorithm is more suitable for reference laboratories to identify Shigella spp. and EIEC up to the serotype level.

Foot-and-mouth disease (FMD) is one of the most important livestock diseases in East Africa with outbreaks reported annually that cause severe economic losses. It is possible to control disease using vaccination, but antigenic matching of the vaccine to circulating strains is critical. To determine the relationship between foot-and-mouth disease viruses circulating in districts along the Uganda and Tanzanian border between 2016 and 2017 and currently used vaccines, phylogenetic analysis of the full VP1 virus sequences was carried out on samples collected from both sides of the border. A total of 43 clinical samples were collected from animals exhibiting signs of FMD and VP1 sequences generated from 11 of them. Eight out of the 11 sequences obtained belonged to serotype O and three belonged to serotype A. The serotype O sequences obtained showed limited nucleotide divergence (average of 4.9%) and belonged to topotype East Africa-2, whereas the most common O-type vaccine strain used in the region (O/KEN/77/78) belonged to East Africa-1. The serotype A viruses belonged to topotype Africa-G1 (average nucleotide divergence 7.4%), as did vaccine strain K5/1980. However, vaccine strain K35/1980 belonged to Africa G VII with an average sequence divergence of 20.5% from the study sequences. The genetic distances between current vaccine strains and circulating field strains underscores the crucial need for regular vaccine matching and the importance of collaborative efforts for better control of FMD along this border area.

Background Behcet’s disease (BD) is a recalcitrant, multisystemic inflammatory disease that can lead to irreversible blindness. Microbial agents have been considered to contribute to the pathogenesis of this disease, but the underlying mechanisms remain unclear. In this study, we investigated the association of gut microbiome composition with BD as well as its possible roles in the development of this disease. Methods Fecal and saliva samples were collected from 32 active BD patients and 74 healthy controls. DNA extracted from fecal samples was subjected to metagenomic analysis, whereas DNA extracted from saliva samples was subjected to 16S rRNA gene sequencing analysis. The results were used to compare the composition and biological function of the microbiome between patients and healthy controls. Lastly, transplantation of pooled fecal samples from active BD patients into B10RIII mice undergoing experimental autoimmune uveitis (EAU) was performed to determine the causal relationship between the gut microbiome and BD. Results Fecal samples from active BD patients were shown to be enriched in Bilophila spp., a sulfate-reducing bacteria (SRB) and several opportunistic pathogens (e.g., Parabacteroides spp. and Paraprevotella spp.) along with a lower level of butyrate-producing bacteria (BPB) Clostridium spp. and methanogens (Methanoculleus spp. Methanomethylophilus spp.). Analysis of microbial functions revealed that capsular polysaccharide transport system, oxidation-reduction process, type III, and type IV secretion systems were also increased in active BD patients. Network analysis showed that the BD-enriched SRB and opportunistic pathogens were positively correlated with each other, but they were negatively associated with the BPB and methanogens. Animal experiments revealed that fecal microbiota transplantation with feces from BD patients significantly exacerbated EAU activity and increased the production of inflammatory cytokines including IL-17 and IFN-γ. Conclusions Our findings revealed that BD is associated with considerable gut microbiome changes, which is corroborated by a mouse study of fecal microbiota transplants. A model explaining the association of the gut microbiome composition with BD pathogenesis is proposed. Electronic supplementary material The online version of this article (10.1186/s40168-018-0520-6) contains supplementary material, which is available to authorized users.

International audience; Zoantharians represent a group of marine invertebrates widely distributed from shallow waters to the deep sea. Despite a high diversity and abundance in the rocky reefs of the Pacific Ocean, very few studies have been reported on the diversity of this group in the Tropical Eastern Pacific coasts. While molecular techniques recently clarified some taxonomic relationships within the order, the taxonomy of zoantharians is still highly challenging due to a lack of clear morphological characters and confusing use of different data in previous studies. Our first insight into the zoantharian diversity at El Pelado Marine Protected Area-Ecuador led to the identification of six species: Terrazoanthus patagonichus; Terrazoanthus sp.; Antipathozoanthus hickmani; Parazoanthus darwini; Zoanthus cf. pulchellus; and Zoanthus cf. sociatus. A metabolomic approach using UHPLC-HRMS was proven to be very efficient as a complementary tool in the systematics of these species and specialized metabolites of the ecdysteroid and alkaloid families were identified as key biomarkers for interspecific discrimination. These results show good promise for an application of this integrative approach to other zoantharians.

International audience; A total of 125 Streptomyces strains were isolated from an Algerian wetland (Fetzara Lake) and characterized by growth on different culture media.Phylogenetic analyses were carried out by 16S rRNA sequence comparison after PCR amplification using universal primers. Antibacterial bioassays performed by the agar diffusion method enabled us to retain 33 Streptomyces isolates for their activity against two Gram-positive bacteria (Bacillus subtilis and Micrococcus luteus) and one Gram-negative bacteria (Escherichia coli).Among them, six isolates inhibited all three indicator strains. Antibacterial compounds were then extracted from the solid culture media with ethanol and ethyl acetate as organic solvents. The minimal inhibitory concentration (% v/v) of the extracts was evaluated by a standardized broth dilution method against different clinical-resistant bacterial isolates and Candida albicans.The most active crude extracts were selected for further characterization by chromatographic analysis (RP-HPLC).; Cent vingt-cinq souches de Streptomyces ont été collectées dans une région humide d’Algérie (lac Fetzara) et caractérisées par leur croissance sur différents milieux.Des analyses phylogénétiques ont été réalisées sur la collection à partir de la séquence codant l’ARN 16S après amplification PCR avec des amorces universelles.Des tests d’activités antibactériennes par la méthode de diffusion en agar ont permis de retenir 33 souches pour leurs activités contre deux bactéries à Gram positif (Bacillus subtilis et Micrococcus luteus) et une à Gram négatif (Escherichia coli). Parmi ces souches, six inhibent la croissance des trois souches indicatrices. Les molécules responsables des activités antibactériennes observées ont été extraites du milieu de croissance solide avec des solvants organiques comme l’éthanol et l’acétate d’éthyle. La concentration minimale inhibitrice (% v/v) des extraits a été évaluée par la méthode standardisée de dilution en milieu liquide contre différents isolats bactériens cliniques résistants et contre Candida albicans. Les extraits les plus actifs ont été analysés par chromatographie haute pression (RP-HPLC).

Cyanobacteria provide an interesting platform for biotechnological applications due to their efficient photoautotrophic growth, amenability to genetic engineering and the ability to grow on non-arable land. An ideal industrial strain of cyanobacteria would need to be fast growing and tolerant to high levels of temperature, light, carbon dioxide, salt and be naturally transformable. In this study, we report Synechococcus elongatus PCC 11801, a strain isolated from India that fulfills these requirements. The physiological and biochemical characteristics of PCC 11801 under carbon and light-limiting conditions were investigated. PCC 11801 shows a doubling time of 2.3 h, that is the fastest growth for any cyanobacteria reported so far under ambient CO2 conditions. Genome sequence of PCC 11801 shows genome identity of ~83% with its closest neighbors Synechococcus elongatus PCC 7942 and Synechococcus elongatus UTEX 2973. The unique attributes of PCC 11801 genome are discussed in light of the physiological characteristics that are needed in an industrial strain. The genome of PCC 11801 shows several genes that do not have homologs in neighbor strains PCC 7942 and UTEX 2973, some of which may be responsible for adaptation to various abiotic stresses. The remarkably fast growth rate of PCC 11801 coupled with its robustness and ease of genetic transformation makes it an ideal candidate for the photosynthetic production of fuels and chemicals.

International audience; Members of the genus Dickeya are plant pathogens that mostly cause soft-rot diseases. Diversity within the genus has led to the recent description of three novel species (i.e. a mainly clonal D. solani of economic consequence in potatoes, D. aquatica from water samples and D. fangzhongdai isolated from necrotic pear trees in China). However, multilocus sequence analysis (MLSA) has highlighted the occurrence of seven isolates not related to the defined Dickeya species. These include a previously unclassified group of Dickeya strains isolated from monocotyledonous plants, Dickeya sp. S1, Dickeya sp. B16, and Dickeya sp. NCPPB 3274, as well as Dickeya sp. MK7, a strain isolated from water, and misassigned strains D. solani ND14, D. solani M005 and D. chrysanthemi M074. Here, it is reported that these isolates can be classified as D. fangzhongdai by using average nucleotide identity analysis and MLSA. However, variations in phenotypic characterization featuring colony morphology and carbon utilization assays revealed a diversity of bacterial isolates classified as D. fangzhongdai. Based on the results of the genomic analysis, the classification of Dickeya sp. S1, Dickeya sp. B16, Dickeya sp. MK7, Dickeya sp. NCPPB 3274 to D. fangzhongdai is proposed as well as the reclassification of D. solani ND14, D. solani M005 and D. chrysanthemi M074 to D. fangzhongdai.

Following a request from the European Commission, the EFSA Panel on Plant Health performed a pest categorisation of Arceuthobium spp. (non-EU), a well-defined and distinguishable group of parasitic plant species of the family Viscaceae, also known as dwarf mistletoes. These are flowering plants parasitising a wide range of conifers of the families Pinaceae and Cupressaceae. Arceuthobium species (non-EU) are regulated in Council Directive 2000/29/EC (Annex IAI) as harmful organisms whose introduction into the EU is banned. Many Arceuthobium species are recognised, with most dwarf mistletoes native in the New World, and north-western Mexico and the western USA as the centre of diversity for the genus. Only two Arceuthobium species are native (and reported to be present) in the EU (Arceuthobium azoricum and Arceuthobium oxycedrum), which are thus not part of this pest categorisation. Hosts of non-EU dwarf mistletoes include species of the genera Abies, Cupressus, Juniperus, Larix, Picea, Pinus, Pseudotsuga and Tsuga. Most Arceuthobium spp. can parasitise more than one species of conifer host. Dwarf mistletoes could enter the EU via host plants for planting and cut branches, but these pathways are closed. They could establish in the EU, as hosts are widespread and climatic conditions are favourable. They would be able to spread following establishment by human movement of host plants for planting and cut branches, as well as natural spread. Should non-EU dwarf mistletoes be introduced in the EU, impacts can be expected on coniferous woodlands, plantations, ornamental trees and nurseries. The main uncertainties concern (i) the precise distribution and host range of the individual Arceuthobium spp. and (ii) the level of susceptibility of conifers native to Europe. For Arceuthobium spp. (non-EU) as a group of organisms, the criteria assessed by the Panel for consideration as a potential quarantine pest are met, while, for regulated non-quarantine pests, the criterion on the pest presence in the EU is not met. (C) 2018 European Food Safety Authority. EFSA Journal published by John Wiley and Sons Ltd on behalf of European Food Safety Authority.

We investigated the phylogeography and speciation of Drilus in the Mediterranean, with focus on the Aegean and especially Crete. Altogether 12 species were sequenced for two fragments of the cytochrome c oxidase subunit I gene (cox1-3 ' and cox1-5 ' mtDNA) and provided 1381 nucleotides. Both fragments were analysed under the maximum likelihood criterion and Bayesian inference separately and concatenated as a single dataset. The Drilus species from the Peloponnese, the Ionian islands and Crete did not form a monophylum. Drilus sp. E from the Peloponnese and Zakynthos was sister to D. mauritanicus Lucas from Spain in most cases. The remaining Greek Drilus species formed a robustly supported clade in all analyses; however, the species from Crete do not seem to be monophyletic. Estimating species divergences using BEAST, we found out that the key dates in the west Aegean Drilus phylogeography appeared to be the Tortonian Crete-Peloponnese separation (12-9 Mya), the desiccation of the Mediterranean basin during the Messinian Salinity Crisis (5.96-5.33 Mya), and the repeated fragmentation of Crete during the Pliocene and Pleistocene. Within the Drilus lineages, we obtained a substitution rate estimate of 2.75% divergence per million years, which is in excellent agreement with previous studies. A Generalized Mixed Yule Coalescent (GMYC) analysis suggested the presence of six Drilus species in Crete (seven species in total, since the DNA sequences were not available for D. creticus Pic); however, we formally identified and (re)described only four which can be morphologically defined: D. creticus, D. longulus Kiesenwetter, D. horasfakionus sp. nov. and D. baenai sp. nov. These species are endemic to Crete and surrounding islets. Their diagnostic characters are illustrated and an identification key to males of these species is provided. The intraspecific variability, distribution and ecology of all species are discussed and suggestions for further research are given.[GRAPHICS]

Legume subfamily Caesalpinioideae accommodates approximately 2250 species in 171 genera which traditionally are placed in four tribes: Caesalpinieae, Cassieae, Cercideae and Detarieae. The monophyletic tribe Detarieae includes the Amherstieae subclade which contains about 55 genera. Our knowledge of the relationships among those genera is good in some cases but for many other genera phylogenetic relationships have been unclear. The non-monophyletic nature of at least two amherstioid genera, Cynometra and Hymenostegia has also complicated the picture. During the course of a multi-disciplinary study of Hymenostegia sensu lato, which includes phylogenetic analyses based on matK and trnL data, we have recovered the “Scorodophloeus clade”, an exclusively tropical African clade of four genera which includes the eponymous genus Scorodophloeus, two undescribed generic segregates of Hymenostegia sensu lato, and the previously unsampled rare monospecific genus Micklethwaitia from Mozambique. Zenkerella is suggested as a possible sister genus to the Scorodophloeus clade. A distribution map is presented of the seven species that belong to the Scorodophloeus clade.

Several molecular taxonomic studies have revealed that many natural (wild) Lactococcus lactis strains of dairy origin which are phenotypically representative of the L. lactis subspecies lactis cluster genotypically within subspecies cremoris and vice versa . Recently, we isolated two wild nisin-producing (Nis + ) L. lactis strains, M78 and M104, of the lactis phenotype from Greek raw milk (J. Samelis, A. Lianou, A. Kakouri, C. Delbès, I. Rogelj, B. B. Matijašic, and M. C. Montel, J. Food Prot. 72:783–790, 2009); strain M78 possess a novel nisin A sequence (GenBank accession number HM219853 ). In this study, the actual subspecies identity of M78 and M104 isolates was elucidated, using 16S rRNA and acmA (encoding lactococcal N -acetylmuramidase) gene and histidine biosynthesis operon polymorphisms and 16S rRNA and ldh (encoding lactate dehydrogenase) gene phylogenies. Except the acmA gene analysis, molecular tools revealed that isolates M78 and M104 clustered with strains of the cremoris genotype, including the LMG 6897 T strain, while they were distant from strains of the lactis genotype, including the LMG 6890 T strain. The two wild isolates had identical repetitive sequence-based PCR (rep-PCR), randomly amplified polymorphic DNA (RAPD), plasmid, and whole-cell protein profiles and shared high 16S rRNA (99.9%) and ldh (100%) gene sequence homologies. In contrast, they exhibited identical sugar fermentation and enzymatic patterns which were similar to those of the subspecies lactis LMG 6890 T strain. To our knowledge, this is the first complete identification report on a wild L. lactis subsp. cremoris genotype of the lactis phenotype which is capable of nisin A production and, thus, has strong potential for use as a novel dairy starter and/or protective culture.

Marine lakes are unique ecosystems that contain isolated populations of marine organisms. Isolated from the surrounding marine habitat, many lakes house numerous endemic species. In this study, microbial communities of sponges inhabiting these lakes were investigated for the first time using barcoded pyrosequencing of 16S rRNA gene amplicons. Our main goals were to compare the bacterial richness and composition of two sponge species (Suberites diversicolor and Cinachyrella australiensis) inhabiting both marine lakes and adjacent open coastal systems. Host species and habitat explained almost 59% of the variation in bacterial composition. There was a significant difference in composition between both host species. Within S. diversicolor, there was little discernible difference between bacterial communities inside and outside lakes. The bacterial community of this species was, furthermore, dominated (63% of all sequences) by three very closely related alphaproteobacterial taxa identified as belonging to the recently described order Kiloniellales. Cinachyrella australiensis, in contrast, hosted markedly different bacterial communities inside and outside lakes with very few shared abundant taxa. Cinachyrella australiensis in open habitat only shared 9.4% of OTUs with C. australiensis in lake habitat. Bacteria were thus both highly species specific and, in the case of C. australiensis, habitat specific. Research was funded by Project LESS CORAL – FCOMP01-0124-FEDER013994, refª PTDC/AAC-AMB/115304/ 2009, Project PEst-C/MAR/LA0017/2011, cofunded by both the Portuguese Foundation for Science and Technology and COMPETE (POFC) and The Netherlands Organisation for Scientific Research (ALW #817.01.008, Rubicon #825.12.007). The Indonesian Institute of Sciences (PPO-LIPI) and the Indonesian State Ministry of Research and Technology (RISTEK) provided the research permits in Indonesia. published

Co-infections with HIV and HCV are very frequent among people who inject drugs (PWID). However, very few studies comparatively reconstructed the transmission patterns of both viruses in the same population. We have recruited 117 co-infected PWID during a recent HIV outbreak in Romania. Phylogenetic analyses were performed on HIV and HCV sequences in order to characterize and compare transmission dynamics of the two viruses. Three large HIV clusters (2 subtype F1 and one CRF14_BG) and thirteen smaller HCV transmission networks (genotypes 1a, 1b, 3a, 4a and 4d) were identified. Eighty (65%) patients were both in HIV and HCV transmission chains and 70 of those shared the same HIV and HCV cluster with at least one other patient. Molecular clock analysis indicated that all identified HIV clusters originated around 2006, while the origin of the different HCV clusters ranged between 1980 (genotype 1b) and 2011 (genotypes 3a and 4d). HCV infection preceded HIV infection in 80.3% of cases. Coincidental transmission of HIV and HCV was estimated to be rather low (19.65%) and associated with an outbreak among PWID during detention in the same penitentiary. This study has reconstructed and compared the dispersion of these two viruses in a PWID population. © 2017 Paraschiv et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.