The Entomopathogenic Bacterial Endosymbionts Xenorhabdus and Photorhabdus: Convergent Lifestyles from Divergent Genomes

Members of the genus Xenorhabdus are entomopathogenic bacteria that associate with nematodes. The nematode-bacteria pair infects and kills insects, with both partners contributing to insect pathogenesis and the bacteria providing nutrition to the nematode from available insect-derived nutrients. The nematode provides the bacteria with protection from predators, access to nutrients, and a mechanism of dispersal. Members of the bacterial genus Photorhabdus also associate with nematodes to kill insects, and both genera of bacteria provide similar services to their different nematode hosts through unique physiological and metabolic mechanisms. We posited that these differences would be reflected in their respective genomes. To test this, we sequenced to completion the genomes of Xenorhabdus nematophila ATCC 19061 and Xenorhabdus bovienii SS-2004. As expected, both Xenorhabdus genomes encode many anti-insecticidal compounds, commensurate with their entomopathogenic lifestyle. Despite the similarities in lifestyle between Xenorhabdus and Photorhabdus bacteria, a comparative analysis of the Xenorhabdus, Photorhabdus luminescens, and P. asymbiotica genomes suggests genomic divergence. These findings indicate that evolutionary changes shaped by symbiotic interactions can follow different routes to achieve similar end points

Characterizing the microbiota across the gastrointestinal tract of a Brazilian Nelore steer

The gastrointestinal tracts (GIT) of herbivores harbor dense and diverse microbiota that has beneficial interactions with the host, particularly for agriculturally relevant animals like ruminants such as cattle. When assessing ruminant health, microbiological indicators are often derived from the rumen or feces. However, it is probable that ruminal and fecal microbiota do not reflect the microbial communities within the GIT of ruminants. To test this, we investigated the compartments of the GIT from a Brazilian Nelore steer and performed a 16S rRNA pyrosequencing analysis on the collected samples. Our results showed high intra-individual variation, with samples clustering according to their location in the GIT including the forestomach, small intestine, and large intestine. Although sequences related to the phyla Firmicutes and Bacteroidetes predominated all samples, there was a remarkable variation at the family level. Comparisons between the microbiota in the rumen, feces, and other GIT components showed distinct differences in microbial community. This work is the first intensive non-culture based GIT microbiota analysis for any ruminant and provides a framework for understanding how host microbiota impact the health of bovines

The Genome Sequences of <em>Cellulomonas fimi</em> and “<em>Cellvibrio gilvus”</em> Reveal the Cellulolytic Strategies of Two Facultative Anaerobes, Transfer of “<em>Cellvibrio gilvus</em>” to the Genus <em>Cellulomonas</em>, and Proposal of <em>Cellulomonas gilvus</em> sp. nov

<div><p>Actinobacteria in the genus <em>Cellulomonas</em> are the only known and reported cellulolytic facultative anaerobes. To better understand the cellulolytic strategy employed by these bacteria, we sequenced the genome of the <em>Cellulomonas fimi</em> ATCC 484^T. For comparative purposes, we also sequenced the genome of the aerobic cellulolytic “<em>Cellvibrio gilvus”</em> ATCC 13127^T. An initial analysis of these genomes using phylogenetic and whole-genome comparison revealed that “<em>Cellvibrio gilvus”</em> belongs to the genus <em>Cellulomonas</em>. We thus propose to assign “<em>Cellvibrio gilvus”</em> to the genus <em>Cellulomonas</em>. A comparative genomics analysis between these two <em>Cellulomonas</em> genome sequences and the recently completed genome for <em>Cellulomonas flavigena</em> ATCC 482^T showed that these cellulomonads do not encode cellulosomes but appear to degrade cellulose by secreting multi-domain glycoside hydrolases. Despite the minimal number of carbohydrate-active enzymes encoded by these genomes, as compared to other known cellulolytic organisms, these bacteria were found to be proficient at degrading and utilizing a diverse set of carbohydrates, including crystalline cellulose. Moreover, they also encode for proteins required for the fermentation of hexose and xylose sugars into products such as ethanol. Finally, we found relatively few significant differences between the predicted carbohydrate-active enzymes encoded by these <em>Cellulomonas</em> genomes, in contrast to previous studies reporting differences in physiological approaches for carbohydrate degradation. Our sequencing and analysis of these genomes sheds light onto the mechanism through which these facultative anaerobes degrade cellulose, suggesting that the sequenced cellulomonads use secreted, multidomain enzymes to degrade cellulose in a way that is distinct from known anaerobic cellulolytic strategies.</p> </div

Phylogenetic placement of “<i>Cellvibrio gilvus</i>”.

<p>Rooted Bayesian trees based on 16S rRNA gene sequences (A) and 32 concatenated house-keeping protein sequences (B) showing the relationship between “<i>Cellvibrio gilvus”</i> and sequenced bacterial genomes in the phylum Actinobacteria and Gammaproteobacteria and species within the <i>Cellulomonas</i> and <i>Cellvibrio</i> genera. Bar, 0.1 substitutions per amino acid position.</p

Ortholog analysis of the three <i>Cellulomonas</i> genomes conducted using OrthoMCL.

<p>The total numbers of shared proteins between the three genomes were tabulated and presented as a Venn diagram in (A). The unique proteins from each species were analyzed using the KEGG database (B).</p