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The early detection of spoilage microorganisms and food pathogens is of paramount importance in food production systems. We propose a novel strategy for the early detection of food production defects, harnessing the product microbiome. We hypothesize that by establishing microbiome datasets of proper and defective batches, indicator bacteria signaling production errors can be identified and targeted for rapid quantification as part of routine practice. Using the production process of pastrami as a model, we characterized its live microbiome profiles throughout the production stages and in the final product, using propidium monoazide treatment followed by 16S rDNA sequencing. Pastrami demonstrated product-specific and consistent microbiome profiles predominated by Serratia and Vibrionimonas , with distinct microbial signatures across the production stages. Based on the established microbiome dataset, we were able to detect shifts in the microbiome profile of a defective batch produced under lactate deficiency. The most substantial changes were observed as increased relative abundances of Vibrio and Lactobacillus , which were subsequently defined as potential lactate-deficiency indicators. PMA-qPCR efficiently detected increased levels of these species, thus proving useful in rapidly pinpointing the production defect. This approach offers the possibility of the in-house detection of defective production events with same-day results, promoting safer food production systems.

The emergence and dissemination of antibiotic resistance genes (ARGs) in the ecosystem are global public health concerns. One Health emphasizes the interconnectivity between different habitats and seeks to optimize animal, human, and environmental health. However, information on the dissemination of antibiotic resistance genes (ARGs) within complex microbiomes in natural habitats is scarce. We investigated the prevalence of antibiotic resistant bacteria (ARB) and the spread of ARGs in intensive bullfrog (Rana catesbeiana) farms in the Shantou area of China. Antibiotic susceptibilities of 361 strains, combined with microbiome analyses, revealed Escherichia coli, Edwardsiella tarda, Citrobacter and Klebsiella sp. as prevalent multidrug resistant bacteria on these farms. Whole genome sequencing of 95 ARB identified 250 large plasmids that harbored a wide range of ARGs. Plasmid sequences and sediment metagenomes revealed an abundance of tetA, sul1, and aph(3″)-Ib ARGs. Notably, antibiotic resistance (against 15 antibiotics) highly correlated with plasmid-borne rather than chromosome-borne ARGs. Based on sequence similarities, most plasmids (62%) fell into 32 distinct groups, indicating a potential for horizontal plasmid transfer (HPT) within the frog farm microbiome. HPT was confirmed in inter- and intra-species conjugation experiments. Furthermore, identical mobile ARGs, flanked by mobile genetic elements (MGEs), were found in different locations on the same plasmid, or on different plasmids residing in the same or different hosts. Our results suggest a synergy between MGEs and HPT to facilitate ARGs dissemination in frog farms. Mining public databases retrieved similar plasmids from different bacterial species found in other environmental niches globally. Our findings underscore the importance of HPT in mediating the spread of ARGs in frog farms and other microbiomes of the ecosystem., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Current prebiotics are predominantly carbohydrates. However, great competition exists among gut microbes for the scarce protein in the colon, as most consumed protein is digested and absorbed in the small intestine. Herein we evaluated in-vivo novel next-generation prebiotics: protein-containing-prebiotics, for selectively-targeted delivery of protein to colonic probiotics, to boost their growth. This system is based on micellar-particles, composed of Maillard-glycoconjugates of 2'-Fucosyllactose (2'-FL, human-milk-oligosaccharide) shell, engulfing lactoferrin peptic-then-tryptic hydrolysate (LFH) core. This core-shell structure lowers protein-core digestibility, while the prebiotic glycans are hypothesized to serve as molecular-recognition ligands for selectively targeting probiotics. To study the efficacy of this novel prebiotic, we fed C57BL/6JRccHsd mice with either 2'-FL-LFH Maillard-glycoconjugates, unconjugated components (control), or saline (blank). Administration of 2'-FL-LFH significantly increased the levels of short-chain-fatty-acids (SCFAs)-producing bacterial families (Ruminococcaceae, Lachnospiraceae) and genus (Odoribacter) and the production of the health-related metabolites, SCFAs, compared to the unconjugated components and to saline. The SCFAs-producing genus Prevotella significantly increased upon 2'-FL-LFH consumption, compared to only moderate increase in the unconjugated components. Interestingly, the plasma-levels of inflammation-inducing lipopolysaccharides (LPS), which indicate increased gut-permeability, were significantly lower in the 2'-FL-LFH group compared to the unconjugated-components and the saline groups. We found that Maillard-glycoconjugates of 2'-FL-LFH can serve as novel protein-containing prebiotics, beneficially modulating gut microbial composition and its metabolic activity, thereby contributing to host health more effectively than the conventional carbohydrate-only prebiotics., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Sourdough starters harbor microbial consortia that benefit the final product's aroma and volume. The complex nature of these spontaneously developed communities raises challenges in predicting the fermentation phenotypes. Herein, we demonstrated for the first time in this field the potential of genome-scale metabolic modeling (GEMs) in the study of sourdough microbial communities. Broad in-silico modeling of microbial growth was applied on communities composed of yeast (Saccharomyces cerevisiae) and different Lactic Acid Bacteria (LAB) species, which mainly predominate in sourdough starters. Simulations of model-represented communities associated specific bacterial compositions with sourdough phenotypes. Based on ranking the phenotypic performances of different combinations, Pediococcus spp. - Lb. sakei group members were predicted to have an optimal effect considering the increase in S. cerevisiae growth abilities and overall CO 2 secretion rates. Flux Balance Analysis (FBA) revealed mutual relationships between the Pediococcus spp. - Lb. sakei group members and S. cerevisiae through bidirectional nutrient dependencies, and further underlined that these bacteria compete with the yeast over nutrients to a lesser extent than the rest LAB species. Volatile compounds (VOCs) production was further modeled, identifying species-specific and community-related VOCs production profiles. The in-silico models' predictions were validated by experimentally building synthetic sourdough communities and assessing the fermentation phenotypes. The Pediococcus spp. - Lb. sakei group was indeed associated with increased yeast cell counts and fermentation rates, demonstrating a 25 % increase in the average leavening rates during the first 10 fermentation hours compared to communities with a lower representation of these group members. Overall, these results provide a possible novel strategy towards the de-novo design of sourdough starter communities with tailored-made characterizations, including a shortened leavening period., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

A two-step sequential strategy involving a biocatalytic dehydrogenation/remote hydrofunctionalization, as a unified and versatile approach to selectively convert linear alkanes into a large array of valuable functionalized aliphatic derivatives is reported. The dehydrogenation is carried out by a mutant strain of a bacteria Rhodococcus and the produced alkenes are subsequently engaged in a remote functionalization through a metal-catalyzed hydrometalation/migration sequence that subsequently react with a large variety of electrophiles. The judicious implementation of this combined biocatalytic and organometallic approach enabled us to develop a high-yielding protocol to site-selectively functionalize unreactive primary C-H bonds., (© 2023 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

Objective: Anti-drug antibodies (ADA) to anti-tumour necrosis factor (anti-TNF) therapy drive treatment loss of response. An association between intestinal microbial composition and response to anti-TNF therapy was noted. We therefore aimed to assess the implications of antibiotic treatments on ADA formation in patients with inflammatory bowel disease (IBD)., Design: We analysed data from the epi-IIRN (epidemiology group of the Israeli IBD research nucleus), a nationwide registry of all patients with IBD in Israel. We included all patients treated with anti-TNF who had available ADA levels. Survival analysis with drug use as time varying covariates were used to assess the association between antibiotic use and ADA development. Next, specific pathogen and germ-free C57BL mice were treated with respective antibiotics and challenged with infliximab. ADA were assessed after 14 days., Results: Among 1946 eligible patients, with a median follow-up of 651 days from initiation of therapy, 363 had positive ADA. Cox proportional hazard model demonstrated an increased risk of ADA development in patients who used cephalosporins (HR=1.97, 95% CI 1.58 to 2.44), or penicillins with β-lactamase inhibitors (penicillin-BLI, HR=1.4, 95% CI 1.13 to 1.74), whereas a reduced risk was noted in patients treated with macrolides (HR=0.38, 95% CI 0.16 to 0.86) or fluoroquinolones (HR=0.20, 95% CI 0.12 to 0.35). In mice exposed to infliximab, significantly increased ADA production was observed in cephalosporin as compared with macrolide pretreated mice. Germ-free mice produced no ADA., Conclusion: ADA production is associated with the microbial composition. The risk of ADA development during anti-TNF therapy can possibly be reduced by avoidance of cephalosporins and penicillin-BLIs, or by treatment with fluoroquinolones or macrolides., Competing Interests: Competing interests: YC received research grants, speaker and advisory fees from AbbVie; speaker and advisory fees from Janssen; grant, speaker and advisory fees from Takeda and consultancy fees from CytoReason. SSO received grant funding from Takeda, holds equity and receives consultancy fees from CytoReason. SG-V declares CytoReason advisory fees for last 3 years. RK received consultation fee, research grant, royalties or honorarium from Takeda and Pfizer. ID received consultation fee, research grant or honorarium from Janssen, AbbVie, Takeda, Pfizer, Roche/Genentech, Celgene/BMS, Arena, Neopharm, Gilead, Gallapagos, Celltrion, Ferring, Falk Pharma, MSD, DSM, Cambridge Healthcare, Sublimity, Sangamo, Nestle, Wild bio, Food Industries Association, Integran Holdings, Abbott, Altman Research, (© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)