Thousands of Pristionchus pacificus orphan genes were integrated into developmental networks that respond to diverse environmental microbiota.

Adaptation of organisms to environmental change may be facilitated by the creation of new genes. New genes without homologs in other lineages are known as taxonomically-restricted orphan genes and may result from divergence or de novo formation. Previously, we have extensively characterized the evolution and origin of such orphan genes in the nematode model organism Pristionchus pacificus. Here, we employ large-scale transcriptomics to establish potential functional associations and to measure the degree of transcriptional plasticity among orphan genes. Specifically, we analyzed 24 RNA-seq samples from adult P. pacificus worms raised on 24 different monoxenic bacterial cultures. Based on coexpression analysis, we identified 28 large modules that harbor 3,727 diplogastrid-specific orphan genes and that respond dynamically to different bacteria. These coexpression modules have distinct regulatory architecture and also exhibit differential expression patterns across development suggesting a link between bacterial response networks and development. Phylostratigraphy revealed a considerably high number of family- and even species-specific orphan genes in certain coexpression modules. This suggests that new genes are not attached randomly to existing cellular networks and that integration can happen very fast. Integrative analysis of protein domains, gene expression and ortholog data facilitated the assignments of biological labels for 22 coexpression modules with one of the largest, fast-evolving module being associated with spermatogenesis. In summary, this work presents the first functional annotation for thousands of P. pacificus orphan genes and reveals insights into their integration into environmentally responsive gene networks.

Corrigendum: A MALDI-TOF MS library for rapid identification of human commensal gut bacteria from the class Clostridia.

[This corrects the article DOI: 10.3389/fmicb.2023.1104707.].

A MALDI-TOF MS library for rapid identification of human commensal gut bacteria from the class Clostridia.

Introduction: Microbial isolates from culture can be identified using 16S or whole-genome sequencing which generates substantial costs and requires time and expertise. Protein fingerprinting via Matrix-assisted Laser Desorption Ionization-time of flight mass spectrometry (MALDI-TOF MS) is widely used for rapid bacterial identification in routine diagnostics but shows a poor performance and resolution on commensal bacteria due to currently limited database entries. The aim of this study was to develop a MALDI-TOF MS plugin database (CLOSTRI-TOF) allowing for rapid identification of non-pathogenic human commensal gastrointestinal bacteria. Methods: We constructed a database containing mass spectral profiles (MSP) from 142 bacterial strains representing 47 species and 21 genera within the class Clostridia. Each strain-specific MSP was constructed using >20 raw spectra measured on a microflex Biotyper system (Bruker-Daltonics) from two independent cultures. Results: For validation, we used 58 sequence-confirmed strains and the CLOSTRI-TOF database successfully identified 98 and 93% of the strains, respectively, in two independent laboratories. Next, we applied the database to 326 isolates from stool of healthy Swiss volunteers and identified 264 (82%) of all isolates (compared to 170 (52.1%) with the Bruker-Daltonics library alone), thus classifying 60% of the formerly unknown isolates. Discussion: We describe a new open-source MSP database for fast and accurate identification of the Clostridia class from the human gut microbiota. CLOSTRI-TOF expands the number of species which can be rapidly identified by MALDI-TOF MS.

Correction: Bacterial vitamin B12 production enhances nematode predatory behavior.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Bacterial vitamin B12 production enhances nematode predatory behavior.

Although the microbiota is known to affect host development, metabolism, and immunity, its impact on host behavior is only beginning to be understood. In order to better characterize behavior modulation by host-associated microorganisms, we investigated how bacteria modulate complex behaviors in the nematode model organism Pristionchus pacificus. This nematode is a predator that feeds on the larvae of other nematodes, including Caenorhabditis elegans. By growing P. pacificus on different bacteria and testing their ability to kill C. elegans, we reveal large differences in killing efficiencies, with a Novosphingobium species showing the strongest enhancement. This enhanced killing was not accompanied by an increase in feeding, which is a phenomenon known as surplus killing, whereby predators kill more prey than necessary for sustenance. Our RNA-seq data demonstrate widespread metabolic rewiring upon exposure to Novosphingobium, which facilitated screening of bacterial mutants with altered transcriptional responses. We identified bacterial production of vitamin B12 as an important cause of such enhanced predatory behavior. Although vitamin B12 is an essential cofactor for detoxification and metabolite biosynthesis, shown previously to accelerate development in C. elegans, supplementation with this enzyme cofactor amplified surplus killing in P. pacificus, whereas mutants in vitamin B12-dependent pathways reduced surplus killing. By demonstrating that production of vitamin B12 by host-associated microbiota can affect complex host behaviors, we reveal new connections between animal diet, microbiota, and nervous system.

Culture-based analysis of Pristionchus-associated microbiota from beetles and figs for studying nematode-bacterial interactions.

The interplay with bacteria is of crucial importance for the interaction of multicellular organisms with their environments. Studying the associations between the nematode model organisms Caenorhabditis elegans and Pristionchus pacificus with bacteria constitutes a powerful system to investigate these interactions at a mechanistic level. P. pacificus is found in association with scarab beetles in nature and recent studies revealed the succession and dynamics of this nematode and its microbiome during the decomposition of one particular host species, the rhinoceros beetle Oryctes borbonicus on La Réunion Island. However, these studies were performed using culture-free methods, with no attempt made to establish bacterial cultures from the beetle-nematode ecosystem and to investigate the effects of these microbes on life history traits in P. pacificus. Here, we establish and characterize a collection of 136 bacterial strains that have been isolated from scarab beetles and figs, another Pristionchus-associated environment, as a resource for studying their effect on various nematode traits. Classification based on 16S sequencing identified members of four bacterial phyla with the class of Gammaproteobacteria representing the majority with 81 strains. Assessing the survival of P. pacificus on individual bacteria allowed us to propose candidate groups of pathogens such as Bacillaceae, Actinobacteria, and Serratia. In combination with chemoattraction data, it was revealed that P. pacificus is able to recognize and avoid certain groups of pathogens, but not others. Our collection of bacterial strains forms a natural resource to study the effects of bacterial diet on development and other traits. Furthermore, these results will form the basis of future studies to elucidate the molecular mechanisms of recognition and pathogenicity.