Search

Definition: Saccharomyces cerevisiae (SC), a yeast with an extensive history in food and beverage fermentations, is increasingly acknowledged for its multifaceted application in promoting and benefiting all aspects of a 'One Health' approach, including the prevention and control of zoonoses. For instance, SC contributes to environmentally sustainable agricultural practices through the reduced use of toxic agents, thus minimizing air and soil pollution while enhancing crop quality. Additionally, this versatile yeast can improve the health of domestic and farm animals, leading to more efficient and sustainable food production, while fostering synergistic impacts across environmental, animal, and human health spheres. Moreover, SC directly applies benefits to human health by promoting improved nutrition, improving gut health through probiotics, as an alternative to antibiotics, and treating gastric disorders. By aligning with several Sustainable Development Goals (SDGs), SC is vital in advancing global health and well-being, environmental sustainability, and responsible consumption and production. This entry illustrates the numerous benefits of SC and highlights its significant impact on a global 'One Health' scale, promoting the achievement of SDGs through its unique characteristics and deeper understanding of its contribution to the One Health concept. [ABSTRACT FROM AUTHOR]

Shotgun metagenomic sequencing is a common approach for studying the taxonomic diversity and metabolic potential of complex microbial communities. Current methods primarily use second generation short read sequencing, yet advances in third generation long read technologies provide opportunities to overcome some of the limitations of short read sequencing. Here, we compared seven platforms, encompassing second generation sequencers (Illumina HiSeq 300, MGI DNBSEQ-G400 and DNBSEQ-T7, ThermoFisher Ion GeneStudio S5 and Ion Proton P1) and third generation sequencers (Oxford Nanopore Technologies MinION R9 and Pacific Biosciences Sequel II). We constructed three uneven synthetic microbial communities composed of up to 87 genomic microbial strains DNAs per mock, spanning 29 bacterial and archaeal phyla, and representing the most complex and diverse synthetic communities used for sequencing technology comparisons. Our results demonstrate that third generation sequencing have advantages over second generation platforms in analyzing complex microbial communities, but require careful sequencing library preparation for optimal quantitative metagenomic analysis. Our sequencing data also provides a valuable resource for testing and benchmarking bioinformatics software for metagenomics. Measurement(s) mock community • Metagenomic profiling Technology Type(s) Illumina HiSeq 3000 • ThermoFisher Ion Proton and GeneStudio S5 • MGI DNBseq G400 and T7 • Oxford Nanopore Sequencing • PacBio Sequel System • Genome mapping and assembly Sample Characteristic - Organism Synthetic microbial communities • Bacteria • Archaea [ABSTRACT FROM AUTHOR]

Background: Diosmectite, a natural colloidal clay, has been used worldwide for a number of approved indications, including the treatment of chronic functional diarrhea. Here, we used high-resolution whole metagenome shotgun sequencing to assess the impact of a 5 weeks administration of diosmectite (3 g/sachet, 3 sachets/day) on the fecal microbiota of 35 adults with functional chronic diarrhea. Results: Gut microbiota was not impacted by diosmectite administration. In particular, richness remained stable and no microbial species displayed a significant evolution. Segregating patients either by diosmectite response (non responder, early responder, late responder) or by nationality (Great-Britain or Netherlands) yielded the same results. Conclusion: We concluded that no microbiota-related physiological alterations are expected upon long-term treatment with diosmectite. Trial registration: Clinicaltrials.gov NCT03045926 [ABSTRACT FROM AUTHOR]

The development of reliable, mixed-culture biotechnological processes hinges on understanding how microbial ecosystems respond to disturbances. Here we reveal extensive phenotypic plasticity and niche complementarity in oleaginous microbial populations from a biological wastewater treatment plant. We perform meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics) on in situ samples over 14 months at weekly intervals. Based on 1,364 de novo metagenome-assembled genomes, we uncover four distinct fundamental niche types. Throughout the time-series, we observe a major, transient shift in community structure, coinciding with substrate availability changes. Functional omics data reveals extensive variation in gene expression and substrate usage amongst community members. Ex situ bioreactor experiments confirm that responses occur within five hours of a pulse disturbance, demonstrating rapid adaptation by specific populations. Our results show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity, and set the foundation for future ecological engineering efforts. Herold et al. present an integrated meta-omics framework to investigate how mixed microbial communities, such as oleaginous bacterial populations in biological wastewater treatment plants, respond with distinct adaptation strategies to disturbances. They show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity. [ABSTRACT FROM AUTHOR]

Mitigation of greenhouse gas emissions is relevant for reducing the environmental impact of ruminant production. In this study, the rumen microbiome from Holstein cows was characterized through a combination of 16S rRNA gene and shotgun metagenomic sequencing. Methane production (CH4) and dry matter intake (DMI) were individually measured over 4–6 weeks to calculate the CH4 yield (CH4y = CH4/DMI) per cow. We implemented a combination of clustering, multivariate and mixed model analyses to identify a set of operational taxonomic unit (OTU) jointly associated with CH4y and the structure of ruminal microbial communities. Three ruminotype clusters (R1, R2 and R3) were identified, and R2 was associated with higher CH4y. The taxonomic composition on R2 had lower abundance of Succinivibrionaceae and Methanosphaera, and higher abundance of Ruminococcaceae, Christensenellaceae and Lachnospiraceae. Metagenomic data confirmed the lower abundance of Succinivibrionaceae and Methanosphaera in R2 and identified genera (Fibrobacter and unclassified Bacteroidales) not highlighted by metataxonomic analysis. In addition, the functional metagenomic analysis revealed that samples classified in cluster R2 were overrepresented by genes coding for KEGG modules associated with methanogenesis, including a significant relative abundance of the methyl‐coenzyme M reductase enzyme. Based on the cluster assignment, we applied a sparse partial least‐squares discriminant analysis at the taxonomic and functional levels. In addition, we implemented a sPLS regression model using the phenotypic variation of CH4y. By combining these two approaches, we identified 86 discriminant bacterial OTUs, notably including families linked to CH4 emission such as Succinivibrionaceae, Ruminococcaceae, Christensenellaceae, Lachnospiraceae and Rikenellaceae. These selected OTUs explained 24% of the CH4y phenotypic variance, whereas the host genome contribution was ~14%. In summary, we identified rumen microbial biomarkers associated with the methane production of dairy cows; these biomarkers could be used for targeted methane‐reduction selection programmes in the dairy cattle industry provided they are heritable. [ABSTRACT FROM AUTHOR]

The mechanism of electron transport across electroactive biofilms (EABs) is of high interest and still a matter of debate. Quantitative assessments of their redox conduction take considerable time and require non-turnover conditions (absence of substrate), which can be detrimental to EABs. Here, we measure the charge-transport parameters of Geobacter spp. dominated EABs with double potential step chronoamperometry (DPSC) with Cottrell analysis. The DPSC measurement is simpler and much faster than usual techniques and allows the determination of the charge-transport parameters even under turnover conditions. The electrochemical responses were well-described by a model of redox conduction driven only by electron diffusion within the EAB. The apparent diffusion coefficient for the electron ( Dapp) was measured as approximately 3.2×10−7 cm2 s−1, a value similar to those recorded for pure Geobacter sulfurreducens EABs, or for some redox polymers with comparable redox center concentrations. This method will be valuable for assessing the impact of EAB characteristics and environmental factors on the charge-transport ability of the biofilm, and for determining the rate-limiting step(s) for current production. [ABSTRACT FROM AUTHOR]

Lactic acid is a high-in-demand chemical, which can be produced through fermentation of lignocellulosic feedstock. However, fermentation of complex substrate produces a mixture of products at efficiencies too low to justify a production process. We hypothesized that the background acetic acid concentration plays a critical role in lactic acid yield; therefore, its retention via selective extraction of lactic acid or its addition would improve overall lactic acid production and eliminate net production of acetic acid. To test this hypothesis, we added 10 g/L of acetate to fermentation broth to investigate its effect on products composition and concentration and bacterial community evolution using several substrate-inoculum combinations. With rumen fluid inoculum, lactate concentrations increased by 80 ± 12 % (cornstarch, p < 0.05) and 16.7 ± 0.4 % (extruded grass, p < 0.05) while with pure culture inoculum ( Lactobacillus delbrueckii and genetically modified (GM) Escherichia coli), a 4 to 23 % increase was observed. Using rumen fluid inoculum, the bacterial community was enriched within 8 days to >69 % lactic acid bacteria (LAB), predominantly Lactobacillaceae. Higher acetate concentration promoted a more diverse LAB population, especially on non-inoculated bottles. In subsequent tests, acetate was added in a semi-continuous percolation system with grass as substrate. These tests confirmed our findings producing lactate at concentrations 26 ± 5 % ( p < 0.05) higher than the control reactor over 20 days operation. Overall, our work shows that recirculating acetate has the potential to boost lactic acid production from waste biomass to levels more attractive for application. [ABSTRACT FROM AUTHOR]

Background: Volatile fatty acids (VFA) are building blocks for the chemical industry. Sustainable, biological production is constrained by production and recovery costs, including the need for intensive pH correction. Membrane electrolysis has been developed as an in situ extraction technology tailored to the direct recovery of VFA from fermentation while stabilizing acidogenesis without caustic addition. A current applied across an anion exchange membrane reduces the fermentation broth (catholyte, water reduction: H2O + e- → ½ H2 + OH-) and drives carboxylate ions into a clean, concentrated VFA stream (anolyte, water oxidation: H2O → 2e- + 2 H+ + O2). Results: In this study, we fermented thin stillage to generate a mixed VFA extract without chemical pH control. Membrane electrolysis (0.1 A, 3.22 ± 0.60 V) extracted 28 ± 6 % of carboxylates generated per day (on a carbon basis) and completely replaced caustic control of pH, with no impact on the total carboxylate production amount or rate. Hydrogen generated from the applied current shifted the fermentation outcome from predominantly C2 and C3 VFA (64 ± 3 % of the total VFA present in the control) to majority of C4 to C6 (70 ± 12 % in the experiment), with identical proportions in the VFA acid extract. A strain related to Megasphaera elsdenii (maximum abundance of 57 %), a bacteria capable of producing mid-chain VFA at a high rate, was enriched by the applied current, alongside a stable community of Lactobacillus spp. (10 %), enabling chain elongation of VFA through lactic acid. A conversion of 30 ± 5 % VFA produced per sCOD fed (60 ± 10 % of the reactive fraction) was achieved, with a 50 ± 6 % reduction in suspended solids likely by electro-coagulation. Conclusions: VFA can be extracted directly from a fermentation broth by membrane electrolysis. The electrolytic water reduction products are utilized in the fermentation: OH- is used for pH control without added chemicals, and H2 is metabolized by species such as Megasphaera elsdenii to produce greater value, more reduced VFA. Electrofermentation displays promise for generating added value chemical co-products from biorefinery sidestreams and wastes. [ABSTRACT FROM AUTHOR]

High-throughput sequencing of ribosomal RNA gene (rDNA) amplicons has opened up the door to large-scale comparative studies of microbial community structures. The short reads currently produced by massively parallel sequencing technologies make the choice of sequencing region crucial for accurate phylogenetic assignments. While for 16S rDNA, relevant regions have been well described, no truly systematic design of 18S rDNA primers aimed at resolving eukaryotic diversity has yet been reported. Here we used 31,862 18S rDNA sequences to design a set of broad-taxonomic range degenerate PCR primers. We simulated the phylogenetic information that each candidate primer pair would retrieve using paired- or single-end reads of various lengths, representing different sequencing technologies. Primer pairs targeting the V4 region performed best, allowing discrimination with paired-end reads as short as 150 bp (with 75% accuracy at genus level). The conditions for PCR amplification were optimised for one of these primer pairs and this was used to amplify 18S rDNA sequences from isolates as well as from a range of environmental samples which were then Illumina sequenced and analysed, revealing good concordance between expected and observed results. In summary, the reported primer sets will allow minimally biased assessment of eukaryotic diversity in different microbial ecosystems. [ABSTRACT FROM AUTHOR]

Mixed microbial communities are complex, dynamic and heterogeneous. It is therefore essential that biomolecular fractions obtained for high-throughput omic analyses are representative of single samples to facilitate meaningful data integration, analysis and modeling. We have developed a new methodological framework for the reproducible isolation of high-quality genomic DNA, large and small RNA, proteins, and polar and non-polar metabolites from single unique mixed microbial community samples. The methodology is based around reproducible cryogenic sample preservation and cell lysis. Metabolites are extracted first using organic solvents, followed by the sequential isolation of nucleic acids and proteins using chromatographic spin columns. The methodology was validated by comparison to traditional dedicated and simultaneous biomolecular isolation methods. To prove the broad applicability of the methodology, we applied it to microbial consortia of biotechnological, environmental and biomedical research interest. The developed methodological framework lays the foundation for standardized molecular eco-systematic studies on a range of different microbial communities in the future. [ABSTRACT FROM AUTHOR]

Introduction: Increased adiposity, dyslipidemia and insulin resistance are associated with increased risk of developing cardiometabolic diseases (CM). Such deleterious phenotypes have been shown to be associated with a low gene-richness microbiota that can partly be restored by a short-term dietary intervention (energy-restricted high-protein diet, low glycemic index, enrichment with fibers) in parallel to an improvement of CM profile. In this study, we aimed at increasing fiber intake in quantity and diversity through a two-month consumption of bread enriched with a mix of selected fibers and evaluated the impact of this dietary intervention on gut microbiota gene richness and CM risk profile in subjects at risk of developing CM. Materials and methods: In a randomized double blind cross-over design, thirty-nine subjects with CM risk profile (18–70 years old, BMI: 25–35 kg/m2, waist circumference > 80 cm for women and > 96 cm for men, fiber intake < 20g/day, low fiber diversity) consumed daily for 8 weeks 150 g of standard bread vs. 150 g of bread enriched with a 7-selected fibers mix (5.55 g vs. 16.35 g of fiber respectively; 4-week washout). Gut microbiota and CM risk factors' analyzes were conducted before and after intervention. Stool samples were analyzed by shotgun metagenomics; microbial genes and metagenomics species (MSP) profiles were generated by mapping reads on a reference genes catalog (1529 MSP). Results: The included dyslipidemic subjects with CM risk profile presented a lower microbiota gene richness compared to reference healthy cohorts. The two-month consumption of fiber-rich bread did not alter microbiota gene richness but modified microbiota composition with a significant decrease of Bacteroides vulgatus (q = 1.7e-4) and a significant increase of Parabacteroides distasonis (q = 2.8e-6), Fusicatenibacter saccharivorans (q = 5e-5) and Clostridiales (q = 3.8e-2). We observed in parallel a significant decrease in total cholesterol (- 0.26 mmol/L; - 5%; p = 0.021), LDL-cholesterol (- 0.2 mmol/L; - 6%, p = 0.0061) and an improvement of insulin sensibility estimated by HOMA index (3.23–2.54 mUI/L; - 21%; p = 0.0079).These effects were even significantly more pronounced for subjects presenting the higher waist circumference. Anthropometric parameters were not altered. Discussion: The enrichment of the diet with a mix of selected fibers for 2 months altered microbiota composition by modifying the relative abundance of specific gut bacterial species, in parallel to a significant improvement of cholesterol and insulin sensitivity parameters. Increasing the quantity and diversity of dietary fiber intake could be used as an efficient tool to favorably impact CM profile. [ABSTRACT FROM AUTHOR]

Introduction: Increased adiposity, dyslipidemia and insulin resistance are associated with increased risk of developing cardiometabolic diseases (CM). Such deleterious phenotypes have been shown to be associated with a low gene-richness microbiota that can partly be restored by a short-term dietary intervention (energy-restricted high-protein diet, low glycemic index, enrichment with fibers) in parallel to an improvement of CM profile. In this study, we aimed at increasing fiber intake in quantity and diversity through a two-month consumption of bread enriched with a mix of selected fibers and evaluated the impact of this dietary intervention on gut microbiota gene richness and CM risk profile in subjects at risk of developing CM. Materials and methods: In a randomized double blind cross-over design, thirty-nine subjects with CM risk profile (18–70 years old, BMI: 25–35 kg/m2, waist circumference > 80 cm for women and > 96 cm for men, fiber intake < 20g/day, low fiber diversity) consumed daily for 8 weeks 150 g of standard bread vs. 150 g of bread enriched with a 7-selected fibers mix (5.55 g vs. 16.35 g of fiber respectively; 4-week washout). Gut microbiota and CM risk factors' analyzes were conducted before and after intervention. Stool samples were analyzed by shotgun metagenomics; microbial genes and metagenomics species (MSP) profiles were generated by mapping reads on a reference genes catalog (1529 MSP). Results: The included dyslipidemic subjects with CM risk profile presented a lower microbiota gene richness compared to reference healthy cohorts. The two-month consumption of fiber-rich bread did not alter microbiota gene richness but modified microbiota composition with a significant decrease of Bacteroides vulgatus (q = 1.7e-4) and a significant increase of Parabacteroides distasonis (q = 2.8e-6), Fusicatenibacter saccharivorans (q = 5e-5) and Clostridiales (q = 3.8e-2). We observed in parallel a significant decrease in total cholesterol (- 0.26 mmol/L; - 5%; p = 0.021), LDL-cholesterol (- 0.2 mmol/L; - 6%, p = 0.0061) and an improvement of insulin sensibility estimated by HOMA index (3.23–2.54 mUI/L; - 21%; p = 0.0079).These effects were even significantly more pronounced for subjects presenting the higher waist circumference. Anthropometric parameters were not altered. Discussion: The enrichment of the diet with a mix of selected fibers for 2 months altered microbiota composition by modifying the relative abundance of specific gut bacterial species, in parallel to a significant improvement of cholesterol and insulin sensitivity parameters. Increasing the quantity and diversity of dietary fiber intake could be used as an efficient tool to favorably impact CM profile. [ABSTRACT FROM AUTHOR]

Akkermansia muciniphila, an abundant mucin degrading intestinal bacterium, has been correlated with human health in various studies. The in vitro SHIME model was used to reach a mechanistic understanding of A. muciniphila's colonization preferences and its response to environmental parameters such as colon pH and mucins. These insight can help to identify the optimal conditions for successful in vivo application. After a period of mucin deprivation, we found that mucin supplementation resulted in significantly different microbial communities, with more Akkermansia, Bacteroides and Ruminococcus. Mucin treatment accounted for 26% of the observed variation in the microbial community at OTU level (P = 0.001), whereas the donor effect was limited (8%) (P = 0.035), indicating mucins to constitute an important ecological niche shaping the microbiota composition. The effect of colonic pH had a less profound impact on the microbiome with both pH and donor origin explaining around 10% of the variability in the dataset. Yet, higher simulated colonic pH had a positive impact on Akkermansia abundance while short chain fatty acid analysis displayed a preference for propionate production with higher colonic pH. Our results show that mucins as nutritional resource are a more important modulator of the gut microbiome than colon pH as environmental factor. [ABSTRACT FROM AUTHOR]

Long-term human Space missions depend on regenerative life support systems (RLSS) to produce food, water and oxygen from waste and metabolic products. Microbial biotechnology is efficient for nitrogen conversion, with nitrate or nitrogen gas as desirable products. A prerequisite to bioreactor operation in Space is the feasibility to reactivate cells exposed to microgravity and radiation. In this study, microorganisms capable of essential nitrogen cycle conversions were sent on a 44-days FOTON-M4 flight to Low Earth Orbit (LEO) and exposed to 10−3-10−4 g (gravitational constant) and 687 ± 170 µGy (Gray) d−1 (20 ± 4 °C), about the double of the radiation prevailing in the International Space Station (ISS). After return to Earth, axenic cultures, defined and reactor communities of ureolytic bacteria, ammonia oxidizing archaea and bacteria, nitrite oxidizing bacteria, denitrifiers and anammox bacteria could all be reactivated. Space exposure generally yielded similar or even higher nitrogen conversion rates as terrestrial preservation at a similar temperature, while terrestrial storage at 4 °C mostly resulted in the highest rates. Refrigerated Space exposure is proposed as a strategy to maximize the reactivation potential. For the first time, the combined potential of ureolysis, nitritation, nitratation, denitrification (nitrate reducing activity) and anammox is demonstrated as key enabler for resource recovery in human Space exploration. [ABSTRACT FROM AUTHOR]

The Back Cover picture illustrates the discharge of an electroactive biofilm recorded by double potential step chronoamperometry, allowing the fast determination of charge‐transfer parameters across the biofilm (Artwork: A. Landi). More information can be found in the Article by A. Prévoteau and co‐workers on page 1026 in Issue 5, 2017 (DOI: 10.1002/celc.201600853). [ABSTRACT FROM AUTHOR]