Alterations in human gut microbiome composition and metabolism after exposure to glyphosate and Roundup and/or a spore-based formulation using the SHIME® technology

Despite extensive research into the toxicology of the herbicide glyphosate, there are still major unknowns regarding its effects on the human gut microbiome. As a step in addressing this knowledge gap, we describe for the first time the effects of glyphosate and a Roundup glyphosate-based herbicide on infant gut microbiota using SHIME technology, which mimics the entire gastrointestinal tract. SHIME microbiota culture was undertaken in the presence of a concentration of 100 mg/L (corresponding to a dose of 1.6 mg/kg/day) glyphosate and the same glyphosate equivalent concentration of Roundup, which is in the range of the US chronic reference dose, and subjected to molecular profiling techniques to assess outcomes. Roundup and to a lesser extent glyphosate caused an increase in fermentation activity, resulting in acidification of the microbial environment. This was also reflected by an increase in lactate and acetate production concomitant to a decrease in the levels of propionate, valerate, caproate and butyrate. Ammonium production reflecting proteolytic activities was increased by Roundup exposure. Global metabolomics revealed large scale disturbances in metabolite profiles, including an increased abundance of long chain polyunsaturated fatty acids (n3 and n6). Although changes in bacterial composition measured by qPCR and 16S rRNA sequencing were less clear, our results suggested that lactobacilli had their growth stimulated as a result of microenvironment acidification. Co-treatment with the spore-based probiotic formulation MegaSporeBiotic reverted some of the changes in short-chain fatty acid levels. Altogether, our results suggest that glyphosate can exert effects on human gut microbiota at permitted regulatory levels of exposure, highlighting the need for epidemiological studies aimed at evaluating the effects of glyphosate herbicides on human gut microbiome function.

Accelerated discovery of novel glycoside hydrolases using targeted functional profiling and selective pressure on the rumen microbiome

Background Carbohydrate-active enzymes (CAZymes) form the most widespread and structurally diverse set of enzymes involved in the breakdown, biosynthesis, or modification of lignocellulose that can be found in living organisms. However, the structural diversity of CAZymes has rendered the targeted discovery of novel enzymes extremely challenging, as these proteins catalyze many different chemical reactions and are sourced by a vast array of microbes. Consequently, many uncharacterized members of CAZyme families of interest have been overlooked by current methodologies (e.g., metagenomic screening) used to discover lignocellulolytic enzymes. Results In the present study, we combined phenotype-based selective pressure on the rumen microbiota with targeted functional profiling to guide the discovery of unknown CAZymes. In this study, we found 61 families of glycoside hydrolases (GH) (out of 182 CAZymes) from protein sequences deposited in the CAZy database—currently associated with more than 20,324 microbial genomes. Phenotype-based selective pressure on the rumen microbiome showed that lignocellulolytic bacteria (e.g., Fibrobacter succinogenes, Butyrivibrio proteoclasticus) and three GH families (e.g., GH11, GH13, GH45) exhibited an increased relative abundance in the rumen of feed efficient cattle when compared to their inefficient counterparts. These results paved the way for the application of targeted functional profiling to screen members of the GH11 and GH45 families against a de novo protein reference database comprised of 1184 uncharacterized enzymes, which led to the identification of 18 putative xylanases (GH11) and three putative endoglucanases (GH45). The biochemical proof of the xylanolytic activity of the newly discovered enzyme validated the computational simulations and demonstrated the stability of the most abundant xylanase. Conclusions These findings contribute to the discovery of novel enzymes for the breakdown, biosynthesis, or modification of lignocellulose and demonstrate that the rumen microbiome is a source of promising enzyme candidates for the biotechnology industry. The combined approaches conceptualized in this study can be adapted to any microbial environment, provided that the targeted microbiome is easy to manipulate and facilitates enrichment for the microbes of interest.

Oropharynx microbiota transitions in hypopharyngeal carcinoma treatment of induced chemotherapy followed by surgery

Aims To analyze changes in oropharynx microbiota composition after receiving induced chemotherapy followed by surgery for hypopharyngeal squamous cell carcinoma (HPSCC) patients. Methods Clinical data and swab samples of 38 HPSCC patients (HPSCC group) and 30 patients with benign disease (control group, CG) were enrolled in the study. HPSCC group was stratified into two groups: induced chemotherapy group (IC) of 10 patients and non-induced chemotherapy group (nIC) of 28 patients. The microbiota from oropharyngeal membrane was analyzed through 16S rRNA sequencing. Results Alpha-diversity (Shannon and Ace indexes) and weighted UniFrac based beta-diversity severely decreased in the HPSCC group when compared with CG. In pre-operative comparisons, PCoA and NMDS analyses showed microbial structures in the IC group were more similar to CG than nIC. Both IC group and nIC group yielded significantly diverse post-operative communities in contrast to their pre-operative counterparts, evident by the decrease in genera Veillonella and Fusobacterium and increase in genera Streptococcus and Gemella. Given that post-operative oropharynx microbiota showed no difference between IC and nIC groups, the IC group showed less accumulation in anaerobic communities. The abundance of genera Fusobacterium, Parvimonas, Actinomyces were enhanced in the advanced stages (III/IV). Conclusions Oropharynx microbiota in the HPSCC group presents dysbiosis with low diversity and abundance. Induced chemotherapy is beneficial in adjusting the oropharynx microbial environment leading to fewer amounts of anaerobe accumulation after operation. Higher amounts of Fusobacterium in advanced stages (III/IV) may influence the progression of HPSCC.

263 Characterizing Vaginal Bacterial Community Composition in Brangus Heifers

The role of the reproductive tract microbiota is an emerging field receiving considerable attention in human research, whereby the vaginal microbiota has been characterized in relation to fertility, conception, pregnancy, and parturition. However, the acidic, Lactobaccillus dominated vaginal microbiota in humans contrasts the neutral, dynamic microbial environment characterized in cattle. Over the past few years, many postpartum studies in dairy cattle described a mechanism recently proposed in humans, the ascension of the vaginal microbiota into the uterine body at the onset of labor. Although bovine fetal sterility prior to parturition is under debate, the vaginal microbiota is an early contact for the neonate with microorganisms and inoculates the uterus during parturition. Thus, any changes occurring in the vaginal microbiota could have implications in dam and calf health; this, combined with ease of access, led to the current research focusing on the bovine vaginal microbiota. Characterization studies during the estrous cycle, gestation, and postpartum period have been performed, concluding the bovine vaginal microbiota is dynamic. However, due to the low abundance in the vaginal microbiota, the seemingly small taxonomic changes reported in these studies could be of great importance. Secondly, researchers have begun to evaluate the effect of exogenous and endogenous hormone concentrations on the vaginal microbiota. Little to no differences have been found except with exogenous melatonin supplementation. In pregnant heifers, exogenous melatonin altered the beta diversity of the vaginal tract by increasing aerobic bacteria present. Moreover, a study evaluating the effects of nutrient restriction on the vaginal microbiota found no taxonomic or structure differences. These findings have allowed researchers to target paucities, improve methodology, and realize the importance of the reproductive tract microbiota. In short, based on these studies, future research examining the role of the reproductive tract microbiota could uncover mechanisms vital to increasing reproductive performance.

Bacterial Inhibition on Beauveria bassiana Contributes to Microbiota Stability in Delia antiqua

Given the multiple roles of associated microbiota in improving animal host fitness in a microbial environment, increasing numbers of researchers have focused on how the associated microbiota keeps stable under complex environmental factors, especially some biological ones. Recent studies show that associated microbiota interacts with pathogenic microbes. However, whether and how the interaction would influence microbiota stability is limitedly investigated. Based on the interaction among Delia antiqua, its associated microbiota, and one pathogen Beauveria bassiana, the associated microbiota's response to the pathogen was determined in this study. Besides, the underlying mechanism for the response was also preliminarily investigated. Results showed that B. bassiana neither infect D. antiqua larvae nor did it colonize inside the associated microbiota, and both the bacterial and fungal microbiota kept stable during the interaction. Further experiments showed that bacterial microbiota almost completely inhibited conidial germination and mycelial growth of B. bassiana during its invasion, while fungal microbiota did not inhibit conidial germination and mycelial growth of B. bassiana. According to the above results, individual dominant bacterial species were isolated, and their inhibition on conidial germination and mycelial growth of B. bassiana was reconfirmed. Thus, these results indicated that bacterial instead of fungal microbiota blocked B. bassiana conidia and stabilized the associated microbiota of D. antiqua larvae during B. bassiana invasion. The findings deepened the understanding of the role of associated microbiota–pathogen microbe interaction in maintaining microbiota stability. They may also contribute to the development of novel biological control agents and pest management strategies.

The Role of Fecal Microbiota Transplantation in the Treatment of Inflammatory Bowel Disease

The exact pathogenesis of inflammatory bowel disease (IBD) is still not completely understood. It is hypothesized that a genetic predisposition leads to an exaggerated immune response to an environmental trigger, leading to uncontrolled inflammation. As there is no known causative treatment, current management strategies for inflammatory bowel disease focus on correcting the excessive immune response to environmental (including microbial) triggers. In recent years, there has been growing interest in new avenues of treatment, including targeting the microbial environment itself. Fecal microbiota transplantation (FMT) is a novel treatment modality showing promising results in early studies. The article discusses the rationale for the use of FMT in inflammatory bowel disease and the yet-unresolved questions surrounding its optimal use in practice.