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.

Beneficial effects of pyruvate for a high-density perfusion process

High volumetric productivities can be achieved when perfusion processes are operated at high cell densities. Yet it is fairly challenging to keep high cell density cultures in a steady state over an extended period. Aiming for robust processes, in this study cultures were operated at a constant biomass specific perfusion rate (BSPR). The cell density was monitored with a capacitance probe and a continuous bleed maintained the cell density at the targeted viable cell volume (VCV). Despite our tightly controlled BSPR, a gradual accumulation of ammonium and changes in cell diameter were observed during the production phase for the three different monoclonal antibodies (mAbs). Although a lot of efforts in media optimization have been made to reduce ammonium in fed-batch process, less examples are known about how media components impact the cellular metabolism and thus the quality of monoclonal antibodies in continuous processes. In this work, we show that a continuous Na-pyruvate fed at 2 g/L/day strongly reduced ammonium production and stabilized fucosylation, sialylation and high mannose content for three different mAbs.

Metabolism of Black Carrot Polyphenols during In Vitro Fermentation Is Not Affected by Cellulose or Cell Wall Association

Fruit and vegetable polyphenols are associated with health benefits, and those not absorbed could be fermented by the gastro-intestinal tract microbiota. Many fermentation studies focus on “pure” polyphenols, rather than those associated with plant cell walls (PCW). Black carrots (BlkC), are an ideal model plant food as their polyphenols bind to PCW with minimal release after gastro-intestinal digestion. BlkC were fractionated into three components—supernatant, pellet after centrifugation, and whole puree. Bacterial cellulose (BCell) was soaked in supernatant (BCell&S) as a model substrate. All substrates were fermented in vitro with a pig faecal inoculum. Gas kinetics, short chain fatty acids, and ammonium production, and changes in anthocyanins and phenolic acids were compared. This study showed that metabolism of BlkC polyphenols during in vitro fermentation was not affected by cellulose/cell wall association. In addition, BCell&S is an appropriate model to represent BlkC fermentation, suggesting the potential to examine fermentability of PCW-associated polyphenols in other fruits/vegetables.

Biogenic Fe(II-III) Hydroxycarbonate Green Rust Enhances Nitrate Removal and Decreases Ammonium Selectivity during Heterotrophic Denitrification

Nitrification-denitrification is the most widely used nitrogen removal process in wastewater treatment. However, this process can lead to undesirable nitrite accumulation and subsequent ammonium production. Biogenic Fe(II-III) hydroxycarbonate green rust has recently emerged as a candidate to reduce nitrite without ammonium production under abiotic conditions. The present study investigated whether biogenic iron(II-III) hydroxycarbonate green rust could also reduce nitrite to gaseous nitrogen during bacterial nitrate reduction. Our results showed that biogenic iron(II-III) hydroxycarbonate green rust could efficiently decrease the selectivity of the reaction towards ammonium during heterotrophic nitrate reduction by native wastewater-denitrifying bacteria and by three different species of Shewanella: S. putrefaciens ATCC 12099, S. putrefaciens ATCC 8071 and S. oneidensis MR-1. Indeed, in the absence of biogenic hydroxycarbonate green rust, bacterial reduction of nitrate converted 11–42% of the initial nitrate into ammonium, but this value dropped to 1–28% in the presence of biogenic hydroxycarbonate green rust. Additionally, nitrite accumulation did not exceed the 2–13% in the presence of biogenic hydroxycarbonate green rust, versus 0–28% in its absence. Based on those results that enhance the extent of denitrification of about 60%, the study proposes a water treatment process that couples the bacterial nitrite production with the abiotic nitrite reduction by biogenic green rust.

Coal-Degrading Bacteria Display Characteristics Typical of Plant Growth Promoting Rhizobacteria

Coal mining produces large quantities of discard that is stockpiled in large dumps. This stockpiled material, termed coal discard, poses an environmental threat emphasising the need for appropriate bioremediation. Here, metagenomic analysis of the 16S rRNA from ten coal-degrading strains previously isolated from coal slurry from discard dumps and from the rhizosphere of diesel-contaminated sites was used to establish genetic relatedness to known plant growth-promoting (PGP) bacteria in the NCBI database. Measurement of indole and ammonium production and solubilisation of P and K were used to screen bacteria for PGP characteristics. BLAST analysis revealed ≥ 99% homology of six isolates with reference PGP strains of Bacillus, Escherichia, Citrobacter, Serratia, Exiguobacterium and Microbacterium, while two strains showed 94% and 91% homology with Proteus. The most competent PGP strains were Proteus strain ECCN 20b, Proteus strain ECCN 23b and Serratia strain ECCN 24b isolated from diesel-contaminated soil. In response to L-trp supplementation, the concentration of indolic compounds (measured as indole-3-acetic acid) increased. Production of ammonium and solubilisation of insoluble P by these strains was also apparent. Only Serratia strain ECCN 24b was capable of solubilising insoluble K. Production of indoles increased following exposure to increasing aliquots of coal discard, suggesting no negative effect of this material on indole production by these coal-degrading bacterial isolates and that these bacteria may indeed possess PGP characteristics.

Omeprazole-induced hypomagnesaemia, causing renal tubular acidosis with hypokalaemia, hypocalcaemia, hyperlactacidaemia and hyperammonaemia

A 72-year-old Japanese man treated with omeprazole for 11 years was admitted due to loss of consciousness and muscle weakness. Wolff-Parkinson-White syndrome-induced tachycardia was considered as the cause of syncope. His blood examination revealed rhabdomyolysis, hypokalaemia, hypomagnesaemia, hypocalcaemia, hyperlactacidaemia, hyperammonaemia and high-anion-gap metabolic acidosis. Hypomagnesaemia could be caused by magnesium malabsorption due to omeprazole use. Hypocalcaemia might be caused by the inhibitory effect of hypomagnesemia on the parathyroid gland hormone secretion. Hyperammonaemia might be caused by two reasons: (1) renal ammonium production induced by hypokalaemia; (2) inhibition of ammonium secretion by omeprazole. Both hypocalcaemia and hypokalaemia might cause chronic elevation of serum creatinine phosphokinase which ended up with rhabdomyolysis. Correction of serum electrolytes rapidly improved his muscle weakness. Discontinuation of omeprazole no longer caused these abnormalities. A physician should be aware of unexplained signs and symptoms of patients using proton-pump inhibitors to avoid life-threatening electrolyte and physiologic disturbances.