Ruminants are foregut fermenters that have the remarkable ability of converting plant polymers that are indigestible to humans into assimilable comestibles like meat and milk, which are cornerstones of human nutrition. Ruminants establish a symbiotic relationship with their microbiome, and the latter is the workhorse of carbohydrate fermentation. On the other hand, during carbohydrate fermentation, synthesis of propionate sequesters H, thus reducing its availability for the ultimate production of methane (CH4) by methanogenic archaea. Biochemically, methane is the simplest alkane and represents a downturn in energetic efficiency in ruminants; environmentally, it constitutes a potent greenhouse gas that negatively affects climate change. Prevotella is a very versatile microbe capable of processing a wide range of proteins and polysaccharides, and one of its fermentation products is propionate, a trait that appears conspicuous in P. ruminicola strain 23. Since propionate, but not acetate or butyrate, constitutes an H sink, propionate-producing microbes have the potential to reduce methane production. Accordingly, numerous studies suggest that members of the genus Prevotella have the ability to divert the hydrogen flow in glycolysis away from methanogenesis and in favor of propionic acid production. Intended for a broad audience in microbiology, our review summarizes the biochemistry of carbohydrate fermentation and subsequently discusses the evidence supporting the essential role of Prevotella in lignocellulose processing and its association with reduced methane emissions. We hope this article will serve as an introduction to novice Prevotella researchers and as an update to others more conversant with the topic.

Background/Objectives: Due to the numerical dominance of environmental and commensal strains, understanding antimicrobial resistance (AMR) transmission in Escherichia coli requires consideration of non-clinical as well as pathogenic isolates. In this cross-sectional study, associations between the genetic context of non-clinical E. coli and AMR carriage are examined in isolates sampled from different niches within a One Health continuum. Methods: Two hundred eighty-eight E. coli isolates collected in Alberta, Canada (2018–2019) from wastewater, well water, feces of broiler chickens and feedlot cattle, and retail beef and chicken meat were selected from existing surveillance collections using a stratified random sampling structure. Using short-read whole genome assemblies, phylogenetic relationships were inferred from pan-genome multiple sequence alignments. Principal coordinate analysis and permutational analysis of variance (PERMANOVA) of a Jaccard dissimilarity matrix derived from gene presence/absence data were used to investigate contributions of source and AMR strata to observe genetic dissimilarity. Population clustering and gene under- or over-representation by source and cluster were also explored. Results: Minimal phylogenetic segregation of isolates was noted based on source or AMR strata, and both contributed significant but small proportions of observed genetic dissimilarity, with the largest proportion attributed to phylogroup. There was notable diversity of E. coli within and between sources; however, in some larger clusters, differential gene presence/absence was potentially linked to ecological niche rather than source of isolation. Conclusions: This study highlights the ecological complexity of AMR in E. coli in non-clinical contexts, offering a novel lens on how niche-specific factors can influence population structure and AMR carriage. It also provides insight into apparent discrepancies in the literature regarding clustering of E. coli by source. These findings support a more integrative One Health approach to AMR surveillance, emphasizing the need to account for microbial diversity and niche-specific adaptation across interconnected systems.

Importance: Although highly effective in treating recurrent Clostridioides difficile infection (RCDI), the mechanisms of action of fecal microbial transplantation (FMT) are not fully understood. Aim: The aim of this study was to explore microbially derived products or pathways that could contribute to the therapeutic efficacy of FMT. Methods: Stool shotgun metagenomic sequencing data from 18 FMT-treated RCDI patients at 4 points in time were used for the taxonomic and functional profiling of their gut microbiome. The abundance of the KEGG orthology (KO) groups was subjected to univariate linear mixed models to assess the significance of the observed differences between 0 (pre-FMT), 1, 4, and 12 weeks after FMT. Results: Of the 59,987 KO groups identified by shotgun metagenomic sequencing, 27 demonstrated a statistically significant change after FMT. These KO groups are involved in many cellular processes, including iron homeostasis, glycerol metabolism, and arginine regulation, all of which have been implicated to play important roles in bacterial growth and virulence in addition to modulating the intestinal microbial composition. Conclusion: Our findings suggest potential changes in key KO groups post-FMT, which may contribute to FMT efficacy beyond the restored microbial composition/diversity and metabolism of bile acids and short-chain fatty acids. Future larger studies that include a fecal metabolomics analysis combined with animal model validation work are required to further elucidate the molecular mechanisms.

Meloidogyne causes a devastating disease known as root-knot that affects tomatoes and other cash crops worldwide. Conversely, Paraburkholderia tropica has proven beneficial in mitigating the effects of various pathogens in plants. We aimed to unravel the molecular events that underlie the beneficial effects of the bacterium and the detrimental impacts of the nematode when inoculated separately or together in tomato plants. The transcriptional responses induced by P. tropica (TB group (tomato-bacteria group)), Meloidogyne spp. (TN group (tomato-nematode group)) or by the two agents (TBN group (tomato-bacteria-nematode group)) in tomato were assessed by RNA-seq. We implemented a transcript discovery pipeline which allowed the identification of 2283 putative novel transcripts. Differential expression analysis revealed that upregulated transcripts were much more numerous than downregulated ones. At the gene ontology level, the most activated term was ‘hydrolase activity acting on ester bonds’ in all groups. In addition, when both microbes were inoculated together, ‘hydrolase activity acting on O-glycosyl compounds’ was activated. This finding suggests defense responses related to lipid and carbohydrate metabolism, membrane remodeling and signal transduction. Notably, defense genes, transcription factors and protein kinases stood out. Differentially expressed transcripts suggest the activation of a multifaceted plant defense response against the nematode occurred, which was exacerbated by pre-inoculation of P. tropica.

Core needle biopsy is the gold standard procedure for sampling tissues for pathology-based diagnostics. However, it produces significant tissue damage and may lead to undue pain and risk of complications such as infections. Alternatives such as fine needle aspiration and liquid biopsy have not yet achieved the same widespread utility owing to the limited abundance of cells and relevant biomarkers in extracted sample. Here we introduce a novel shock-scattering micro-histotripsy-aided fine needle aspiration technology which uses cavitation to liquefy microscopic volumes to produce tissue homogenates with both intact and lysed cells. It permits not only conventional cytopathology with high success but sufficient high-quality tissue homogenates to enable reliable ancillary testing such as genetic biomarker profiling and even whole genome sequencing with improved quality compared to formalin-fixed samples. Our approach represents a new paradigm for tissue diagnostics with orders of magnitude less damage than core-needle biopsy procedures.

Root-knot nematodes (Meloidogyne spp.) are the most economically important group of plant-parasitic nematodes worldwide. We tested whether foliar elicitors induce defense enzymes in leaves and reduce nematode reproduction in the roots of the same plants. Tomato cv. Santa Clara, which lacks Mi-1 resistance, received 50 mL per plant of one of six treatments: chitosan at 2.0 or 2.5 mg mL⁻¹, Paraburkholderia tropica GIBI_0183 or Bacillus infantis GIBI_0177 at 2.5 × 10⁷ cells per plant, or a commercial chitosan or Bacillus subtilis product. Each treatment was applied with and without 1000 s-stage juveniles in the soil. β-1,3-Glucanase and chitinase activities were measured in leaves 1, 2, 6 and 8 days after application (n = 10), and eggs in whole root systems at 60 days (n = 6). Leaves sampled on days 1 and 2 were sprayed; those sampled on days 6 and 8 expanded afterward. Both enzymes showed a treatment × day interaction (permutation p = 0.0001). Every treatment reduced the egg count by 63–75% (p ≤ 0.0003), with no differences detected among treatments at the sample size used. All six raised chitinase in plants without nematodes, whereas β-1,3-glucanase fell below the control under both laboratory chitosans, which reduced the egg count as much as the treatments that raised it. Enzyme induction and nematode suppression are separate outcomes.