Microbes are the most abundant and diverse organisms on Earth. In contrast to macroscopic organisms, their environmental preferences and ecological interdependencies remain difficult to assess, requiring laborious molecular surveys at diverse sampling sites. Here, we present a global meta-analysis of previously sampled microbial lineages in the environment. We grouped publicly available 16S ribosomal RNA sequences into operational taxonomic units at various levels of resolution and systematically searched these for co-occurrence across environments. Naturally occurring microbes, indeed, exhibited numerous, significant interlineage associations. These ranged from relatively specific groupings encompassing only a few lineages, to larger assemblages of microbes with shared habitat preferences. Many of the coexisting lineages were phylogenetically closely related, but a significant number of distant associations were observed as well. The increased availability of completely sequenced genomes allowed us, for the first time, to search for genomic correlates of such ecological associations. Genomes from coexisting microbes tended to be more similar than expected by chance, both with respect to pathway content and genome size, and outliers from these trends are discussed. We hypothesize that groupings of lineages are often ancient, and that they may have significantly impacted on genome evolution.

/pdf/a-global-network-of-coexisting-microbes-from-environmental-4mts3mey6g.pdf

A global network of coexisting microbes from environmental and whole-genome sequence data

https://www.jidonline.org/article/S0022-202X(15)35036-3/pdf

Diversity of the human skin microbiome early in life

Among the Gram-positive anaerobic bacteria associated with clinical infections, the Gram-positive anaerobic cocci (GPAC) are the most prominent and account for approximately 25-30% of all isolated anaerobic bacteria from clinical specimens. Still, routine culture and identification of these slowly growing anaerobes to the species level has been limited in the diagnostic laboratory, mainly due to the requirement of prolonged incubation times and time-consuming phenotypic identification. In addition, GPAC are mostly isolated from polymicrobial infections with known pathogens and therefore their relevance has often been overlooked. However, through improvements in diagnostic and in particular molecular techniques, the isolation and identification of individual genera and species of GPAC associated with specific infections have been enhanced. Furthermore, the taxonomy of GPAC has undergone considerable changes over the years, mainly due to the development of molecular identification methods. Existing species have been renamed and novel species have been added, resulting in changes of the nomenclature. As the abundance and significance of GPAC in clinical infections grow, knowledge of virulence factors and antibiotic resistance patterns of different species becomes more important. The present review describes recent advances of GPAC and what is known of the biology and pathogenic effects of Anaerococcus, Finegoldia, Parvimonas, Peptoniphilus and Peptostreptococcus, the most important GPAC genera isolated from human infections.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/1574-6976.12005

Gram-positive anaerobic cocci--commensals and opportunistic pathogens.

Analysis of a newly sequenced bacterial genome starts with identification of protein-coding genes. Functional assignment of proteins requires the exact knowledge of protein N-termini. We present a new program ORPHEUS that identifies candidate genes and accurately predicts gene starts. The analysis starts with a database similarity search and identification of reliable gene fragments. The latter are used to derive statistical characteristics of protein-coding regions and ribosome-binding sites and to predict the complete set of genes in the analyzed genome. In a test on Bacillus subtilis and Escherichia coli genomes, the program correctly identified 93.3% (resp. 96.3%) of experimentally annotated genes longer than 100 codons described in the PIR-International database, and for these genes 96.3% (83.9%) of starts were predicted exactly. Furthermore, 98.9% (99.1%) of genes longer than 100 codons annotated in GenBank were found, and 92.9% (75.7%) of predicted starts coincided with the feature table description. Finally, for the complete gene complements of B.subtilis and E.coli, including genes shorter than 100 codons, gene prediction accuracy was 88.9 and 87.1%, respectively, with 94.2 and 76.7% starts coinciding with the existing annotation.

Combining diverse evidence for gene recognition in completely sequenced bacterial genomes.

Gut microbiome characteristics associated with HIV infection are of intense research interest but a deep understanding has been challenged by confounding factors across studied populations. Notably, a Prevotella-rich microbiome described in HIV-infected populations is now understood to be common in men who have sex with men (MSM) regardless of HIV status, but driving factors and potential health implications are unknown. Here, we further define the MSM-associated gut microbiome and describe compositional differences between the fecal microbiomes of Prevotella-rich MSM and non-MSM that may underlie observed pro-inflammatory properties. Furthermore, we show relatively subtle gut microbiome changes in HIV infection in MSM and women that include an increase in potential pathogens that is ameliorated with antiretroviral therapy (ART). Lastly, using a longitudinal cohort, we describe microbiome changes that happen after ART initiation. This study provides an in-depth characterization of microbiome differences that occur in a US population infected with HIV and demonstrates the degree to which these differences may be driven by lifestyle factors, ART, and HIV infection itself. Understanding microbiome compositions that occur with sexual behaviors that are high risk for acquiring HIV and untreated and ART-treated HIV infection will guide the investigation of immune and metabolic functional implications to ultimately target the microbiome therapeutically.

/pdf/an-exploration-of-prevotella-rich-microbiomes-in-hiv-and-men-3zhz1xu3mc.pdf

An exploration of Prevotella -rich microbiomes in HIV and men who have sex with men

Finegoldia magna (formerly Peptostreptococcus magnus), a member of the Gram-positive anaerobic cocci (GPAC), is a commensal bacterium colonizing human skin and mucous membranes. Moreover, it is also recognized as an opportunistic pathogen responsible for various infectious diseases. Here, we report the complete genome sequence of F. magna ATCC 29328. The genome consists of a 1,797,577 bp circular chromosome and an 189,163 bp plasmid (pPEP1). The metabolic maps constructed based on the genome information confirmed that most F. magna strains cannot ferment most sugars, except fructose, and have various aminopeptidase activities. Three homologs of albumin-binding protein, a known virulence factor useful for antiphagocytosis, are encoded on the chromosome, and one albumin-binding protein homolog is encoded on the plasmid. A unique feature of the genome is that F. magna encodes many sortase genes, of which substrates may be involved in bacterial pathogenesis, such as antiphagocytosis and adherence to the host cell. The plasmid pPEP1 encodes seven sortase and seven substrate genes, whereas the chromosome encodes four sortase and 19 substrate genes. These plasmid-encoded sortases may play important roles in the pathogenesis of F. magna by enriching the variety of cell wall anchored surface proteins.

/pdf/complete-genome-sequence-of-finegoldia-magna-an-anaerobic-4oktadedjn.pdf

Complete genome sequence of Finegoldia magna, an anaerobic opportunistic pathogen.

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Complete genome sequence of Finegoldia magna, an anaerobic opportunistic pathogen.