Microbial genomic taxonomy

A need for a genomic species definition is emerging from several independent studies worldwide. In this commentary paper, we discuss recent studies on the genomic taxonomy of diverse microbial groups and a unified species definition based on genomics. Accordingly, strains from the same microbial species share >95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), >95% identity based on multiple alignment genes, 70% in silico Genome-to-Genome Hybridization similarity (GGDH). Species of the same genus will form monophyletic groups on the basis of 16S rRNA gene sequences, Multilocus Sequence Analysis (MLSA) and supertree analysis. In addition to the established requirements for species descriptions, we propose that new taxa descriptions should also include at least a draft genome sequence of the type strain in order to obtain a clear outlook on the genomic landscape of the novel microbe. The application of the new genomic species definition put forward here will allow researchers to use genome sequences to define simultaneously coherent phenotypic and genomic groups

Marinomonas brasilensis sp. nov., isolated from the coral Mussismilia hispida, and reclassification of Marinomonas basaltis as a later heterotypic synonym of Marinomonas communis

A Gram-negative, aerobic bacterium, designated strain R-40503(T), was isolated from mucus of the reef-builder coral Mussismilia hispida, located in the Sao Sebastiao Channel, Sao Paulo, Brazil. Phylogenetic analyses revealed that strain R-40503(T) belongs to the genus Marinomonas. The 16S rRNA gene sequence similarity of R-40503(T) was above 97% with the type strains of Marinomonas vaga, M. basaltis, M. communis and M. pontica, and below 97% with type strains of the other Marinomonas species. Strain R-40503(T) showed less than 35% DNA-DNA hybridization (DDH) with the type strains of the phylogenetically closest Marinomonas species, demonstrating that it should be classified into a novel species. Amplified fragment length polymorphism (AFLP), chemotaxonomic and phenotypic analyses provided further evidence for the proposal of a novel species. Concurrently, a close genomic relationship between M. basaltis and M. communis was observed. The type strains of these two species showed 78% DDH and 63% AFLP pattern similarity. Their phenotypic features were very similar, and their DNA G+C contents were identical (46.3 mol%). Collectively, these data demonstrate unambiguously that Marinomonas basaltis is a later heterotypic synonym of Marinomonas communis. Several phenotypic features can be used to discriminate between Marinomonas species. The novel strain R-40503(T) is clearly distinguishable from its neighbours. For instance, it shows oxidase and urease activity, utilizes L-asparagine and has the fatty acid C(12:1) 3-OH but lacks C(10:0) and C(12:0). The name Marinomonas brasilensis sp. nov. is proposed, with the type strain R-40503(T) (=R-278(T) =LMG 25434(T) =CAIM 1459(T)). The DNA G+C content of strain R-40503(T) is 46.5 mol%

<i>Vibrio communis</i> sp. nov., isolated from the marine animals <i>Mussismilia hispida, Phyllogorgia dilatata, Palythoa caribaeorum, Palythoa variabilis</i> and <i>Litopenaeus vannamei</i>

Eight Vibrio isolates originating from the marine corals Mussismilia hispida and Phyllogorgia dilatata and the zoanthids Palythoa caribaeorum and Palythoa variabilis in Brazil and the Pacific white shrimp (Litopenaeus vannamei) in Ecuador were studied by means of a polyphasic approach. The novel isolates formed a tight monophyletic group in the genus Vibrio and were closely related to species of the Vibrio harveyi group, to which they showed more than 99?% 16S rRNA gene sequence similarity. Analysis based on concatenated sequences of the following seven genes, 16S rRNA, gyrB, recA, rpoA, topA, pyrH and mreB (5633 bp in length), showed clear separation between the isolates and species of the V. harveyi group. Amplified fragment length polymorphism (AFLP) analysis, performed previously, revealed that a representative isolate of this group, LMG 20370, was clearly separate from known Vibrio species (it belonged to the so-called AFLP cluster A31). DNA–DNA hybridization (DDH) experiments with representative isolates and type strains of the V. harveyi species group revealed high DDH between the novel isolates (more than 74?%) and less than 70?% DDH towards type strains of related Vibrio species, proving the novel species status of the isolates. Phenotypically, the novel species belongs to the arginine dihydrolase (A)-negative, lysine decarboxylase (L)-positive and ornithine decarboxylase (O)-positive (A-/L+/O+) cluster reported previously. Most species of the V. harveyi group (i.e. Vibrio rotiferianus, V. harveyi, V. parahaemolyticus and V. alginolyticus) also belong to this A-/L+/O+ cluster. However, several phenotypic features can be used for the identification of the novel species. In contrast to its closest phylogenetic neighbours, the novel species exhibits esterase (C4) and N-acetyl-ß-glucosaminidase activities, but it does not produce acetoin, does not use citrate, a-ketoglutaric acid or propionic acid and does not ferment melibiose. The novel species can also be differentiated on the basis of the presence of the fatty acids C17?:?0, C17?:?1?8c, iso-C17?:?0 and iso-C13?:?0 and the absence of the fatty acid C18?:?0. The name Vibrio communis sp. nov. is proposed for this taxon. Strain R-40496T (=LMG 25430T =CAIM 1816T) is the type strain

Photobacterium sanctipauli sp nov isolated from bleached Madracis decactis (Scleractinia) in the St Peter & St Paul Archipelago, Mid-Atlantic Ridge, Brazil

Five novel strains of Photobacterium (A-394T, A-373, A-379, A-397 and A-398) were isolated from bleached coralMadracis decactis (scleractinian) in the remote St Peter & St Archipelago (SPSPA), Mid-Atlantic Ridge, Brazil. Healthy M. decactis specimens were also surveyed, but no strains were related to them. The novel isolates formed a distinct lineage based on the 16S rRNA, recA, and rpoA gene sequences analysis. Their closest phylogenetic neighbours were Photobacterium rosenbergii, P. gaetbulicola, and P. lutimaris, sharing 96.6 to 95.8% 16S rRNA gene sequence similarity. The novel species can be differentiated from the closest neighbours by several phenotypic and chemotaxonomic markers. It grows at pH 11, produces tryptophane deaminase, presents the fatty acid C-18:0, but lacks C-16:0 iso. The whole cell protein profile, based in MALDI-TOF MS, distinguished the strains of the novel species among each other and from the closest neighbors. In addition, we are releasing the whole genome sequence of the type strain. The name Photobacterium sanctipauli sp. nov. is proposed for this taxon. The G + C content of the type strain A-394(T) (=LMG27910(T) = CAIM1892(T)) is 48.2 mol%

Genomic and phenotypic attributes of novel salinivibrios from stromatolites, sediment and water from a high altitude lake

Background: Salinivibrios are moderately halophilic bacteria found in salted meats, brines and hypersaline environments. We obtained three novel conspecific Salinivibrio strains closely related to S. costicola, from Socompa Lake, a high altitude hypersaline Andean lake (approx. 3,570 meters above the sea level).Results: The three novel Salinivibrio spp. were extremely resistant to arsenic (up to 200 mM HAsO42-), NaCl (up to 15%), and UV-B radiation (19 KJ/m2, corresponding to 240 minutes of exposure) by means of phenotypic tests. Our subsequent draft genome ionsequencing and RAST-based genome annotation revealed the presence of genes related to arsenic, NaCl, and UV radiation resistance. The three novel Salinivibrio genomes also had the xanthorhodopsin gene cluster phylogenetically related to Marinobacter and Spiribacter. The genomic taxonomy analysis, including multilocus sequence analysis, average amino acid identity, and genome-to-genome distance revealed that the three novel strains belong to a new Salinivibrio species.Conclusions: Arsenic resistance genes, genes involved in DNA repair, resistance to extreme environmental conditions and the possible light-based energy production, may represent important attributes of the novel salinivibrios, allowing these microbes to thrive in the Socompa Lake. © 2014 Gorriti et al.; licensee BioMed Central Ltd.Fil: Gorriti, Marta Fabiana. Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brasil ; Brasil. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Planta Piloto de Procesos Industriales Microbiologicos; ArgentinaFil: Dias, Graciela M.. Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brasil ; BrasilFil: Chimetto, Luciane A.. Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brasil ; BrasilFil: Trindade-Silva, Amaro E.. Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brasil ; BrasilFil: Silva, Bruno S.. Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brasil ; BrasilFil: Mesquita, Milene M.A.. Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brasil ; BrasilFil: Gregoracci, Gustavo B.. Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brasil ; BrasilFil: Farias, Maria Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Planta Piloto de Procesos Industriales Microbiologicos; ArgentinaFil: Thompson, Cristiane C.. Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brasil ; BrasilFil: Thompson, Fabiano L.. Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brasil ; Brasi

Structure and temporal dynamics of the bacterial communities associated to microhabitats of the coral Oculina patagonica

Corals are known to contain a diverse microbiota that plays a paramount role in the physiology and health of holobiont. However, few studies have addressed the variability of bacterial communities within the coral host. In this study, bacterial community composition from the mucus, tissue and skeleton of the scleractinian coral Oculina patagonica were investigated seasonally at two locations in the Western Mediterranean Sea, to further understand how environmental conditions and the coral microbiome structure are related. We used denaturing gradient gel electrophoresis in combination with next-generation sequencing and electron microscopy to characterize the bacterial community. The bacterial communities were significantly different among coral compartments, and coral tissue displayed the greatest changes related to environmental conditions and coral health status. Species belonging to the Rhodobacteraceae and Vibrionaceae families form part of O. patagonica tissues core microbiome and may play significant roles in the nitrogen cycle. Furthermore, sequences related to the coral pathogens, Vibrio mediterranei and Vibrio coralliilyticus, were detected not only in bleached corals but also in healthy ones, even during cold months. This fact opens a new view onto unveiling the role of pathogens in the development of coral diseases in the future.This work was supported by the projects CGL2012-39627-C03-01 and CGL2015-66686-C3-3-P (to JA) of the Spanish Ministry of Economy and Competitiveness, that include FEDER funds from the European Union

Evaluation of appendicitis risk prediction models in adults with suspected appendicitis

Background Appendicitis is the most common general surgical emergency worldwide, but its diagnosis remains challenging. The aim of this study was to determine whether existing risk prediction models can reliably identify patients presenting to hospital in the UK with acute right iliac fossa (RIF) pain who are at low risk of appendicitis. Methods A systematic search was completed to identify all existing appendicitis risk prediction models. Models were validated using UK data from an international prospective cohort study that captured consecutive patients aged 16–45 years presenting to hospital with acute RIF in March to June 2017. The main outcome was best achievable model specificity (proportion of patients who did not have appendicitis correctly classified as low risk) whilst maintaining a failure rate below 5 per cent (proportion of patients identified as low risk who actually had appendicitis). Results Some 5345 patients across 154 UK hospitals were identified, of which two‐thirds (3613 of 5345, 67·6 per cent) were women. Women were more than twice as likely to undergo surgery with removal of a histologically normal appendix (272 of 964, 28·2 per cent) than men (120 of 993, 12·1 per cent) (relative risk 2·33, 95 per cent c.i. 1·92 to 2·84; P < 0·001). Of 15 validated risk prediction models, the Adult Appendicitis Score performed best (cut‐off score 8 or less, specificity 63·1 per cent, failure rate 3·7 per cent). The Appendicitis Inflammatory Response Score performed best for men (cut‐off score 2 or less, specificity 24·7 per cent, failure rate 2·4 per cent). Conclusion Women in the UK had a disproportionate risk of admission without surgical intervention and had high rates of normal appendicectomy. Risk prediction models to support shared decision‐making by identifying adults in the UK at low risk of appendicitis were identified

Mudanças ambientais e desdobramentos evolutivos durante o paleogeno

O Paleogeno é um dos períodos da Era Cenozóica, que se distribui entre 65,5 a 23,03 milhões de anos, se localizando logo após o fim da Era Mesozóica, sucedendo o período Cretáceo. Paleoceno, Eoceno e Oligoceno são as épocas que compõem o Período Paleogeno. O Paleogeno pode ser definido como um período de clima quente quando analisado sob a óptica de toda a história geológica. As médias de temperatura para o período superam as temperaturas médias modernas em cerca de 10°C. Durante o Paleogeno também pode se observar eventos drásticos de aumento da temperatura do planeta, sendo possível traçar um paralelo, com o atual aquecimento global ocasionado pelo aumento da emissão de gases do efeito estufa, resguardado suas claras diferenças. A fronteira entre Cretáceo e Paleogeno se caracteriza pela segunda maior extinção da História Geológica do Planeta. Em conseqüência vivencia uma das mais importantes radiações filogenéticas, em todos os ambientes, em particular nos continentais terrestres, caracterizada pela explosão evolutiva dos mamíferos, que exploravam os nichos ecológicos deixados vagos pelo desaparecimento da maior parte dos arcossauromorfos mesozóicos. Somado a isto, no Paleogeno ocorreram importantes mudanças ambientais, abrangendo aspectos geotectônicos e climáticos, que levaram flora e fauna paleogênicas a sofrerem diversas modificações, a fim de se adaptarem ao novo cenário presente no Planeta

Taxonomy of prokaryontes isolated from cnidarians of São Sebastião, SP, Brasil

Orientadores: Fabiano Lopes Thompson, Marcelo BrocchiTese (doutorado) - Universidade Estadual de Campinas, Instituto de BiologiaResumo: Microrganismos têm um papel fundamental na saúde de cnidários, estabelecendo relações ecológicas diversas, de parasitismo até mutualismo. O conhecimento acerca da diversidade de procariontes associados com cnidários e corais no Brasil ainda é escasso. Este é o primeiro estudo enfocando a caracterização taxonômica de bactérias heterotróficas incluindo fixadoras de nitrogênio (N2) e especialmente vibrios isolados do muco do coral endêmico Mussismilia hispida e de zoantídeos simpátricos Palythoa caribaeorum, Palythoa variabilis e Zoanthus solanderi da região de São Sebastião-SP, Brasil. Ao todo, foram obtidos 488 isolados bacterianos destes cnidários, empregando-se os meios de cultivo Ágar Marinho (AM), Ágar Fixação de Nitrogênio (NFb) e Ágar Tiosulfato-Citrato-Bile-Sacarose (TCBS). Os cnidários foram coletados em três praias (Grande, Portinho e Preta) na região de São Sebastião em 2005 e 2006. A maioria dos isolados obtidos pertenciam à classe Gammaproteobacteria. Mais da metade foram identificados como vibrios com base em sequências parciais do gene 16S rRNA. Vibrios do grupo core corresponderam a 80 % das bactérias potencialmente fixadoras de N2 e revelaram alta similaridade de sequência no gene pyrH com V. harveyi e V. alginolyticus. Dezenove isolados representativos, pertencentes às espécies V. harveyi, V. alginolyticus, V. campbellii e V. parahaemolyticus foram capazes de crescer 6 vezes sucessivas em meio NFb e alguns deles mostraram forte atividade da nitrogenase pelo teste de redução de acetileno (ARA). Cerca de 150 vibrios isolados em TCBS foram caracterizados por meio de sequências de 16S rRNA, recA e pyrH. Os taxa mais abundantes foram V. harveyi, V. rotiferianus, V. campbellii, V. alginolyticus, V. mediterranei (=V. shillonii), V. chagasii, V. tubiashii e uma espécie nova de Vibrio. Com exceção de V. chagasii que foi encontrado apenas no muco de M. hispida, as demais espécies foram observadas nos diferentes hospedeiros, não havendo fortes evidências da presença de espécies hospedeiro-específicas. A variabilidade intra-específica dos vibrios foi avaliada por meio de padrões de banda de elementos palindrômicos extragênicos repetitivos (rep-PCR). Esta análise revelou alta diversidade genômica entre os isolados. Cada isolado apresentava um padrão de rep-PCR distinto, indicando uma grande diversidade de populações co-existindo no mesmo habitat. As identificações geradas pelo rep-PCR concordaram com as identificações obtidas pelo MLSA (Multilocus Sequence Analysis). Diversos isolados de diferentes grupos microbianos apresentaram menos de 97 % de similaridade em sequências do gene 16S rRNA com espécies conhecidas, indicando que elas seriam possíveis espécies novas. Ao todo, sete espécies novas foram descritas por meio da taxonomia polifásica: Marinobacterium coralli sp. nov., Marinomonas brasilensis sp. nov., Photobacterium swingsii sp. nov., P. jeanii sp. nov., Vibrio communis sp. nov., V. variabilis sp. nov. e V. marinum sp. nov. Os dados fenotípicos, quimiotaxonômicos, genotípicos e filogenéticos obtidos a partir da descrição das sete espécies novas demonstraram que há uma ampla variabilidade fenotípica intra-específica. Este estudo determinou a identidade dos principais grupos de bactérias cultivadas do muco de corais, sobretudo, os vibrios. Uma das espécies de vibrios mais abundantes no muco dos corais é V. communis sp. nov. A fixação de N2 representa um fenótipo comum entre as espécies de vibrios estudadas, sugerindo uma função positiva no holobionte.Abstract: Microorganisms have a key role in the health of cnidarians establishing ecologic relationships, of parasitism to mutualism. The knowledge on the diversity of prokaryotes associated with corals in Brazil is very limited. This is the first study on the taxonomic characterization of heterotrophic bacteria, including putative N2-fixing and specially vibrios isolated from mucus of endemic coral Mussismilia hispida and the sympatric zoanthids Palythoa caribaeorum, Palythoa variabilis and Zoanthus solanderi. Cnidarian specimens were isolated in the beaches Grande, Portinho and Preta from São Sebastião region, SP, Brazil, in 2005 and 2006. A total of 488 isolates were obtained using different culture media, i.e. Marine Agar (MA), Nitrogen Fixation (NFb) and Thiosulphate-Citrate- Bile-Sucrose Agar (TCBS). The majority of the isolates fell within the class Gammaproteobacteria and more than half of them were vibrios based on 16S rRNA gene sequences. Based on pyrH gene sequences 80 % of the putative N2-fixing bacteria clustered with the Vibrio core species group (i.e. V. harveyi and V. alginolyticus). Nineteen representative isolates of V. harveyi, V. alginolyticus, V. campbellii and V. parahaemolyticus) were capable of growing six successive times in nitrogen-free medium and some of them showed strong nitrogenase activity by means of the acetylene reduction assay (ARA). About 150 vibrios isolated on TCBS were characterized by means of 16S rRNA, recA and pyrH gene sequences. The most abundant taxa were V. harveyi, V. rotiferianus, V. campbellii, V. alginolyticus, V. mediterranei (=V. shillonii), V. chagasii, V. tubiashii and a new Vibrio species. With the exception of V. chagasii which was found only in the mucus of M. hispida, the other species appeared in different hosts with no strong evidence for the presence of host-specific species. A high genomic diversity was observed using rep-PCR. Each vibrio isolate represented a different co-occuring population, suggesting huge intra-especific diversity. There was a complete agreement between the grouping based on rep-PCR and identification based on MLSA (Multilocus Sequence Analysis). Several isolates had less than 97 % similarity towards know species based on 16S rRNA gene sequence, indicating that they are possibly new species. In total, seven new species were described based on polyphasic taxonomy: Marinobacterium coralli sp. nov., Marinomonas brasilensis sp. nov. Photobacterium swingsii sp. nov., P. jeanii sp. nov., Vibrio communis sp. nov., V. variabilis sp. nov. and V. marinum sp. nov. The new species were characterized by polyphasic taxonomy. Based on phenotypic, chimiotaxonomic, genotypic and phylogenetic data obtained from description of new species, it was demonstrated a huge intra-specific phenotypic variability. This study determined the taxonomic identity of heterotrophic bacteria, especially Vibrio, isolates from cnidarians. V. communis sp. nov. is one of the most frequently found species in the corals. Nitrogen fixation is a common phenotypic trait among vibrios, suggesting that these bacteria may have a positive function in the holobiont.DoutoradoGenetica de MicroorganismosDoutor em Genetica e Biologia Molecula