The classDeltaproteobacteriacomprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylumProteobacteria, it rarely affiliates with other proteobacterial classes and is frequently not recovered as a monophyletic unit in phylogenetic analyses. Indeed, one branch of the classDeltaproteobacteriaencompassingBdellovibrio-like predators was recently reclassified into a separate proteobacterial class, theOligoflexia. Here we systematically explore the phylogeny of taxa currently assigned to these classes using 120 conserved single-copy marker genes as well as rRNA genes. The overwhelming majority of markers reject the inclusion of the classesDeltaproteobacteriaandOligoflexiain the phylumProteobacteria. Instead, the great majority of currently recognized members of the classDeltaproteobacteriaare better classified into four novel phylum-level lineages. We propose the namesDesulfobacterotaphyl. nov. andMyxococcotaphyl. nov. for two of these phyla, based on the oldest validly published names in each lineage, and retain the placeholder name SAR324 for the third phylum pending formal description of type material. Members of the classOligoflexiarepresent a separate phylum for which we propose the nameBdellovibrionotaphyl. nov. based on priority in the literature and general recognition of the genusBdellovibrio. Desulfobacterotaphyl. nov. includes the taxa previously classified in the phylumThermodesulfobacteria, and these reclassifications imply that the ability of sulphate reduction was vertically inherited in theThermodesulfobacteriarather than laterally acquired as previously inferred. Our analysis also indicates the independent acquisition of predatory behaviour in the phylaMyxococcotaandBdellovibrionota, which is consistent with their distinct modes of action. This work represents a stable reclassification of one of the most taxonomically challenging areas of the bacterial tree and provides a robust framework for future ecological and systematic studies.

Birds represent a diverse and evolutionarily successful lineage, occupying a wide range of niches throughout the world. Like all vertebrates, avians harbour diverse communities of microorganisms within their guts, which collectively fulfil important roles in providing the host with nutrition and protection from pathogens. Although many studies have investigated the role of particular microbes in the guts of avian species, there has been no attempt to unify the results of previous, sequence-based studies to examine the factors that shape the avian gut microbiota as a whole. In this study, we present the first meta-analysis of the avian gut microbiota, using 16S rRNA gene sequences obtained from a range of publicly available clone-library and amplicon pyrosequencing data. We investigate community membership and structure, as well as probe the roles of some of the key biological factors that influence the gut microbiota of other vertebrates, such as host phylogeny, location within the gut, diet and association with humans. Our results indicate that, across avian studies, the microbiota demonstrates a similar phylum-level composition to that of mammals. Host bird species is the most important factor in determining community composition, although sampling site, diet and captivity status also contribute. These analyses provide a first integrated look at the composition of the avian microbiota, and serve as a foundation for future studies in this area.

The Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria. In order to address this issue, we investigated the phylogenetic placement of this class in the bacterial domain using 16S and 23S rRNA genes, as well as 120 single-copy marker proteins. Single- and concatenated-marker trees were created using a data set of 4,170 bacterial representatives, including 98 Epsilonproteobacteria. Phylogenies were inferred under a variety of tree building methods, with sequential jackknifing of outgroup phyla to ensure robustness of phylogenetic affiliations under differing combinations of bacterial genomes. Based on the assessment of nearly 300 phylogenetic tree topologies, we conclude that the continued inclusion of Epsilonproteobacteria within the Proteobacteria is not warranted, and that this group should be reassigned to a novel phylum for which we propose the name Epsilonbacteraeota (phyl. nov.). We further recommend the reclassification of the order Desulfurellales (Deltaproteobacteria) to a novel class within this phylum and a number of subordinate changes to ensure consistency with the genome-based phylogeny. Phylogenomic analysis of 658 genomes belonging to the newly proposed Epsilonbacteraeota suggests that the ancestor of this phylum was an autotrophic, motile, thermophilic chemolithotroph that likely assimilated nitrogen from ammonium taken up from the environment or generated from environmental nitrate and nitrite by employing a variety of functional redox modules. The emergence of chemoorganoheterotrophic lifestyles in several Epsilonbacteraeota families is the result of multiple independent losses of various ancestral chemolithoautotrophic pathways. Our proposed reclassification of this group resolves an important anomaly in bacterial systematics and ensures that the taxonomy of Proteobacteria remains robust, specifically as genome-based taxonomies become more common.

Birds represent a diverse and evolutionarily successful lineage, occupying a wide range of niches throughout the world. Like all vertebrates, avians harbour diverse communities of microorganisms within their guts, which collectively fulfil crucial roles in providing the host with nutrition and protection from pathogens. Across the field of avian microbiology knowledge is extremely uneven, with several species accounting for an overwhelming majority of all microbiological investigations. These include agriculturally important birds, such as chickens and turkeys, as well as birds of evolutionary or conservation interest. In our previous study we attempted the first meta-analysis of the avian gut microbiota, using 16S rRNA gene sequences obtained from a range of publicly available data sets. We have now extended our analysis to explore the microbiology of several key species in detail, to consider the avian microbiota within the context of what is known about other vertebrates, and to identify key areas of interest in avian microbiology for future study.

The human gut contains dense and diverse microbial communities which have profound influences on human health. Gaining meaningful insights into these communities requires provision of high quality microbial nucleic acids from human fecal samples, as well as an understanding of the sources of variation and their impacts on the experimental model. We present here a systematic analysis of commonly used microbial DNA extraction methods, and identify significant sources of variation. Five extraction methods (Human Microbiome Project protocol, MoBio PowerSoil DNA Isolation Kit, QIAamp DNA Stool Mini Kit, ZR Fecal DNA MiniPrep, phenol:chloroform-based DNA isolation) were evaluated based on the following criteria: DNA yield, quality and integrity, and microbial community structure based on Illumina amplicon sequencing of the V4 region of bacterial and archaeal 16S rRNA genes. Our results indicate that the largest portion of variation within the model was attributed to differences between subjects (biological variation), with a smaller proportion of variation associated with DNA extraction method (technical variation) and intra-subject variation. A comprehensive understanding of the potential impact of technical variation on the human gut microbiota will help limit preventable bias, enabling more accurate diversity estimates.