Phylogenetic systematics of Butyrivibrio and Pseudobutyrivibrio genomes illustrate vast taxonomic diversity, open genomes and an abundance of carbohydrate-active enzyme family isoforms

Butyrivibrio and Pseudobutyrivibrio dominate in anaerobic gastrointestinal microbiomes, particularly the rumen, where they play a key role in harvesting dietary energy. Within these genera, five rumen species have been classified ( Butyrivibrio fibrisolvens , Butyrivibrio hungatei , Butyrivibrio proteoclasticus , Pseudobutyrivibrio ruminis and Pseudobutyrivibrio xylanivorans ) and more recently an additional Butyrivibrio sp. group was added. Given the recent increase in available genomes, we re-investigated the phylogenetic systematics and evolution of Butyrivibrio and Pseudobutyrivibrio . Across 71 genomes, we show using 16S rDNA and 40 gene marker phylogenetic trees that the current six species designations ( P. ruminis , P. xylanivorans , B. fibrisolvens , Butyrivibrio sp., B. hungatei and B. proteclasticus) are found. However, pangenome analysis showed vast genomic variation and a high abundance of accessory genes (91.50–99.34 %), compared with core genes (0.66–8.50 %), within these six taxonomic groups, suggesting incorrectly assigned taxonomy. Subsequent pangenome accessory genomes under varying core gene cut-offs (%) and average nucleotide identity (ANI) analysis suggest the existence of 42 species within 32 genera. Pangenome analysis of those that still group within B. fibrisolvens , B. hungatei and P. ruminis , based on revised ANI phylogeny, also showed possession of very open genomes, illustrating the diversity that exists even within these groups. All strains of both Butyrivibrio and Pseudobutyrivibrio also shared a broad range of clusters of orthologous genes (COGs) (870), indicating recent evolution from a common ancestor. We also demonstrate that the carbohydrate-active enzymes (CAZymes) predominantly belong to glycosyl hydrolase (GH)2, 3, 5, 13 and 43, with numerous within family isoforms apparent, likely facilitating metabolic plasticity and resilience under dietary perturbations. This study provides a major advancement in our functional and evolutionary understanding of these important anaerobic bacteria.

A new genus of Cepheidae and reassessment of the family (Acari: Oribatida)

The middle-derivative, brachypyline oribatid mite family Cepheidae is rather heterogeneous, but many species, even some genera in this family have been poorly diagnosed. Redefinition of hitherto known taxa is, essential for resolving species identity as well as supraspecific systematics. One of such inadequately described species is Cepheus pustulatus (Pearce, 1910), known from Hawaii, which we redescribe here, and a new genus Roycepheus is proposed, based on this species. Relationships of the genus Roycepheus are addressed using the principles of phylogenetic systematics. A table presents the key differences between genera of Cepheidae, and a diagnostic key to adults of these genera, is provided. We discuss the potential synonymies of Sphodrocepheus with Tritegeus, and Reticulocepheus as well as Oribatodes with Cepheus. However, to confirm these synonymies needs redefinition of these genera and examination of types species.

Phylogenetic systematics of the genera of Thryptocerina Jeannel, 1949 and new species from New Caledonia (Coleoptera, Carabidae, Oodini)

The Oodini precinctive to New Caledonia are reviewed with nine species recognized, of which seven are newly described in two genera. Five species are described in the genus Coptocarpus Chaudoir: C. micropssp. nov., C. erwinisp. nov., C. amieuensissp. nov., C. magnussp. nov., and C. leschenisp. nov. In the genus Adelopomorpha Heller two species, A. tethyssp. nov. and A. tuberculatasp. nov., are described. In order to place cladistically the newly described species in a genus, a phylogenetic analysis of a matrix of 36 characters of adult morphology was conducted including exemplar species of three putative outgroup genera, six putative ingroup thryptocerine oodine genera, and all oodine species from New Caledonia. Results show support for Thryptocerina and monophyly of Adelopomorpha. Hoplolenus LaFerté-Sénectère is not monophyletic and Hoplolenus cyllodinus Fauvel is newly combined as Coptocarpus cyllodinuscomb. nov. New Caledonian species of Coptocarpus form a clade, but the Australian species of the genus included in the analysis are rendered paraphyletic by African and Malagasy genera. Implications of this preliminary study for the classification of Oodini and trends in the evolution of the female reproductive tract are discussed. A key to the New Caledonian species of Oodini is provided.

RECENSIÓN. Foundations of Phylogenetic Systematics.

Durante el congreso Fourth Internacional Meeting on Mesozoic Fishes, organizado recientemente en la Universidad Autónoma de Madrid, el editor alemán Friedrich Pfeil presentó sus últimas novedades, entre las que destaca sin duda el libro aquí comentado. Se trata de la primera traducción al inglés de un libro de gran relevancia que, por haber estado publicado hasta ahora exclusivamente en alemán, no ha encontrado aún la repercusión que merece. Siendo un libro que alcanza elevadas cotas de especialización, no es necesario un gran conocimiento previo para sumergirse en su lectura, ya que el Prof. Wägele realiza una exposición clara y rigurosa, desde lo más general hasta lo más específico, asimilable por cualquier lector interesado en la materia. Nos encontramos ante un curso completo de Sistemática teórica y práctica en un sólo y relativamente breve, dada la amplitud de lo abarcado, volumen. La inferencia filogenética en la clasificación de los organismos es una herramienta indispensable hoy en día en todos los campos de la Biología, incluyendo por supuesto la Paleobiología. De ahí el indudable interés que este libro puede y debe despertar en nuestra comunidad paleontológica.

Phylogenetic systematics of Butyrivibrio and Pseudobutyrivibrio genomes illustrate possession of open genomes rich in orthologous accessory genes with an abundance of carbohydrate-active enzyme isoforms

BackgroundButyrivibrio and Pseudobutyrivibrio dominate in anaerobic gastrointestinal microbiomes, particularly the rumen, where they play a key role in harvesting energy from the diet. Within these genera, 5 rumen species have been classified (B. fibrisolvens, B. hungatei, B. proteoclasticus, P. ruminis and P. xylanivorans); nonetheless, the phylogeny and evolution of these genera is still unclear. Given the recent increase in available genomes, a re-investigation of the phylogenetic systematics and evolution of Butyrivibrio and Pseudobutyrivibrio is timely.ResultsWe show, using both a 16S rDNA and 40 gene marker phylogenetic tree, that 6 species, namely 1. P. ruminis, 2. P. xylanivorans, 3. B. fibrisolvens, 4. Butyrivibrio sp., 5. B. hungatei, and 6. B. proteclasticus likely exist. Pangenome analysis at 100% core definition showed a high abundance of accessory genes (91.50 to 99.34%) compared with core genes (0.66 to 8.50%), illustrating possession of very open genomes. Across the 71 genomes, 870 COGs (clusters of orthologous genes) were shared by all taxa, suggesting evolution through speciation from a common ancestor. Further analysis of Carbohydrate-Active Enzymes (CAZymes) genes show that most are within the accessory genome and orthologous in descent with numerous within-family CAZyme isoforms apparent, CAZyme family tree lineages show that these isoforms largely group according to the 6 species, suggesting extensive horizontal gene transfer within these families.ConclusionsWe show the extensive genomic variation found within Butyrivibrio, and to a lesser extent, Pseudobutyrivibrio. and demonstrate the existence of a new Butyrivibrio species. The Butyrivibrio and Pseudobutyrivibrio genomes are very open with very low % core genomes and high % accessory genomes., and possess a number of GH isoforms that we hypothesise facilitate metabolic plasticity and resilience under dietary perturbations. This study utilizes all currently available genomes and consequently provides a major advancement in our understanding of these important anaerobic bacteria.