Cell factories converting lactate and acetate to butyrate: Clostridium butyricum and microbial communities from dark fermentation bioreactors

Microbial and functional characterization of an allochthonous consortium applied to hydrogen production from Citrus Peel Waste in batch reactor in optimized conditions

Energy recovery from lignocellulosic waste has been studied as an alternative to the problem of inappropriate waste disposal. The present study aimed at characterizing the microbial community and the functional activity of reactors applied to H₂ production through lignocellulosic waste fermentation in optimized conditions. The latter were identified by means of Rotational Central Composite Design (RCCD), applied to optimize allochthonous inoculum concentration (2.32-5.68 gTVS/L of granular anaerobic sludge), pH (4.32-7.68) and Citrus Peel Waste (CPW) concentration (1.55-28.45 g/L). After validation, the conditions identified for optimal H₂ production were 4 gSTV/L of allochthonous inoculum, 29.8 g/L of CPW (substrate) and initial pH of 8.98. In these conditions, 48.47 mmol/L of H₂ was obtained, which is 3.64 times higher than the concentration in unoptimized conditions (13.31 mmol H₂/L using 15 g/L of CPW, 2 gTVS/L of allochthonous inoculum, pH 7.0). Acetogenesis was the predominant pathway, and maximal concentrations of 3,731 mg/L of butyric acid and 3,516 mg/L of acetic acid were observed. Regarding the metataxonomic profile, Clostridium genus was dramatically favored in the optimized condition (79.78%) when compared to the allochthonous inoculum (0.43%). It was possible to identify several genes related to H₂ (i.e dehydrogenases) and volatile fatty acids (VFA) production and with cellulose degradation, especially some CAZymes from the classes Auxiliary Activities, Glycoside Hydrolases and Glycosyl Transferase. By means of differential gene expression it was observed that cellulose degradation and acetic acid production pathways were overabundant in samples from the optimized reactors, highlighting endo-β-1,4-glucanase/cellulose, endo-β-1,4-xylanase, β-glucosidase, β-mannosidase, cellulose β-1,4-cellobiosidase, cellobiohydrolase, and others, as main the functions.

Dynamics of dark fermentation microbial communities in the light of lactate and butyrate production

BACKGROUND

This study focuses on the processes occurring during the acidogenic step of anaerobic digestion, especially resulting from nutritional interactions between dark fermentation (DF) bacteria and lactic acid bacteria (LAB). Previously, we have confirmed that DF microbial communities (MCs) that fed on molasses are able to convert lactate and acetate to butyrate. The aims of the study were to recognize the biodiversity of DF-MCs able and unable to convert lactate and acetate to butyrate and to define the conditions for the transformation.

RESULTS

MCs sampled from a DF bioreactor were grown anaerobically in mesophilic conditions on different media containing molasses or sucrose and/or lactate and acetate in five independent static batch experiments. The taxonomic composition (based on 16S_rRNA profiling) of each experimental MC was analysed in reference to its metabolites and pH of the digestive liquids. In the samples where the fermented media contained carbohydrates, the two main tendencies were observed: (i) a low pH (pH ≤ 4), lactate and ethanol as the main fermentation products, MCs dominated with Lactobacillus, Bifidobacterium, Leuconostoc and Fructobacillus was characterized by low biodiversity; (ii) pH in the range 5.0-6.0, butyrate dominated among the fermentation products, the MCs composed mainly of Clostridium (especially Clostridium_sensu_stricto_12), Lactobacillus, Bifidobacterium and Prevotella. The biodiversity increased with the ability to convert acetate and lactate to butyrate. The MC processing exclusively lactate and acetate showed the highest biodiversity and was dominated by Clostridium (especially Clostridium_sensu_stricto_12). LAB were reduced; other genera such as Terrisporobacter, Lachnoclostridium, Paraclostridium or Sutterella were found. Butyrate was the main metabolite and pH was 7. Shotgun metagenomic analysis of the selected butyrate-producing MCs independently on the substrate revealed C.tyrobutyricum as the dominant Clostridium species. Functional analysis confirmed the presence of genes encoding key enzymes of the fermentation routes.

CONCLUSIONS

Batch tests revealed the dynamics of metabolic activity and composition of DF-MCs dependent on fermentation conditions. The balance between LAB and the butyrate producers and the pH values were shown to be the most relevant for the process of lactate and acetate conversion to butyrate. To close the knowledge gaps is to find signalling factors responsible for the metabolic shift of the DF-MCs towards lactate fermentation. Video Abstract.

A gastrointestinal nematode in pregnant and lactating mice alters maternal and neonatal microbiomes

The maternal microbiome is understood to be the principal source of the neonatal microbiome but the consequences of intestinal nematodes on pregnant and lactating mothers and implications for the neonatal microbiome are unknown. Using pregnant CD1 mice infected with Heligmosomoides bakeri, we investigated the microbiomes in maternal tissues (intestine, vagina, and milk) and in the neonatal stomach using MiSeq sequencing of bacterial 16S rRNA genes. Our first hypothesis was that maternal nematode infection altered the maternal intestinal, vaginal, and milk microbiomes and associated metabolic pathways. Maternal nematode infection was associated with increased beta-diversity and abundance of fermenting bacteria as well as Lactobacillus in the maternal caecum 2 days after parturition, together with down-regulated carbohydrate, amino acid and vitamin biosynthesis pathways. Maternal nematode infection did not alter the vaginal or milk microbiomes. Our second hypothesis was that maternal infection would shape colonization of the neonatal microbiome. Although the pup stomach microbiome was similar to that of the maternal vaginal microbiome, pups of infected dams had higher beta-diversity at day 2, and a dramatic expansion in the abundance of Lactobacillus between days 2 and 7 compared with pups nursing uninfected dams. Our third hypothesis that maternal nematode infection altered the composition of neonatal microbiomes was confirmed as we observed up-regulation of several putatively beneficial microbial pathways associated with synthesis of essential and branched-chain amino acids, vitamins, and short-chain fatty acids. We believe this is the first study to show that a nematode living in the maternal intestine is associated with altered composition and function of the neonatal microbiome.

The Anti-Inflammatory Effect and Mucosal Barrier Protection of Clostridium butyricum RH2 in Ceftriaxone-Induced Intestinal Dysbacteriosis

This study aimed at determining the beneficial effect of Clostridium butyricum (CB) RH2 on ceftriaxone-induced dysbacteriosis. To this purpose, BALB/c mice were exposed to ceftriaxone (400 mg/ml) or not (control) for 7 days, and administered a daily oral gavage of low-, and high-dose CB RH2 (10⁸ and 10¹⁰ CFU/ml, respectively) for 2 weeks. CB RH2 altered the diversity of gut microbiota, changed the composition of gut microbiota in phylum and genus level, decreased the F/B ratio, and decreased the pro-inflammatory bacteria (Deferribacteres, Oscillibacter, Desulfovibrio, Mucispirillum and Parabacteroides) in ceftriaxone-treated mice. Additionally, CB RH2 improved colonic architecture and intestinal integrity by improving the mucous layer and the tight junction barrier. Furthermore, CB RH2 also mitigated intestinal inflammation through decreasing proinflammatory factors (TNF-α and COX-2) and increasing anti-inflammatory factors (IL-10). CB RH2 had direct effects on the expansion of CD4⁺ T cells in Peyer’s patches (PPs) in vitro, which in turn affected their immune response upon challenge with ceftriaxone. All these data suggested that CB RH2 possessed the ability to modulate the intestinal mucosal and systemic immune system in limiting intestinal alterations to relieve ceftriaxone-induced dysbacteriosis.

A review on the factors influencing biohydrogen production from lactate: The key to unlocking enhanced dark fermentative processes

Dark fermentation (DF) is one of the most promising biological methods to produce bio-hydrogen and other value added bio-products from carbohydrate-rich wastes and wastewater. However, process instability and low hydrogen production yields and rates have been highlighted as the major bottlenecks preventing further development. Numerous studies have associated such concerns with the inhibitory activity of lactate-producing bacteria (LAB) against hydrogen producers. However, an increasing number of studies have also shown lactate-based metabolic pathways as the prevailing platform for hydrogen production. This opens a vast potential to develop new strategies to deal with the "Achilles heel" of DF - LAB overgrowth - while untapping high-performance DF. This review discusses the key factors influencing the lactate-driven hydrogen production, paying particular attention to substrate composition, the operating conditions, as well as the microbiota involved in the process and its potential functionality and related biochemical routes. The current limitations and future perspectives in the field are also presented.

Dynamics and Complexity of Dark Fermentation Microbial Communities Producing Hydrogen From Sugar Beet Molasses in Continuously Operating Packed Bed Reactors

This study describes the dynamics and complexity of microbial communities producing hydrogen-rich fermentation gas from sugar-beet molasses in five packed-bed reactors (PBRs). The bioreactors constitute a part of a system producing hydrogen from the by-products of the sugar-beet industry that has been operating continuously in one of the Polish sugar factories. PBRs with different working volumes, packing materials, construction and inocula were tested. This study focused on analysis (based on 16S rRNA profiling and shotgun metagenomics sequencing) of the microbial communities selected in the PBRs under the conditions of high (>100 cm3/g COD of molasses) and low (<50 cm3/g COD of molasses) efficiencies of hydrogen production. The stability and efficiency of the hydrogen production are determined by the composition of dark fermentation microbial communities. The most striking difference between the tested samples is the ratio of hydrogen producers to lactic acid bacteria. The highest efficiency of hydrogen production (130-160 cm3/g COD of molasses) was achieved at the ratios of HPB to LAB ≈ 4:2.5 or 2.5:1 as determined by 16S rRNA sequencing or shotgun metagenomics sequencing, respectively. The most abundant Clostridium species were C. pasteurianum and C. tyrobutyricum. A multiple predominance of LAB over HPB (3:1-4:1) or clostridia over LAB (5:1-60:1) results in decreased hydrogen production. Inhibition of hydrogen production was illustrated by overproduction of short chain fatty acids and ethanol. Furthermore, concentration of ethanol might be a relevant marker or factor promoting a metabolic shift in the DF bioreactors processing carbohydrates from hydrogen-yielding toward lactic acid fermentation or solventogenic pathways. The novelty of this study is identifying a community balance between hydrogen producers and lactic acid bacteria for stable hydrogen producing systems. The balance stems from long-term selection of hydrogen-producing microbial community, operating conditions such as bioreactor construction, packing material, hydraulic retention time and substrate concentration. This finding is confirmed by additional analysis of the proportions between HPB and LAB in dark fermentation bioreactors from other studies. The results contribute to the advance of knowledge in the area of relationships and nutritional interactions especially the cross-feeding of lactate between bacteria in dark fermentation microbial communities.

Effects of α-glyceryl monolaurate on growth, immune function, volatile fatty acids, and gut microbiota in broiler chickens

This study was conducted to determine the effects of dietary addition of α-glyceryl monolaurate (α-GML) on growth performance, immune function, volatile fatty acids production and cecal microbiota in broiler chickens. A total of 480 1-day-old yellow-feathered broilers were randomly assigned in equal numbers to 4 dietary treatments: basal diet (NCO) or supplementations with 30 mg/kg bacitracin (ANT), 500 mg/kg α-GML, or 1,000 mg/kg α-GML (GML2). And, each treatment contained 8 replicates with 15 chickens per replicate. After supplementation with α-GML, the total BW gain and average daily weight gain of broilers increased significantly (P < 0.05) compared with the broilers on the NCO diet. Moreover, compared with the NCO group, higher levels of immune globulin M and immune globulin Y were observed in both GML groups and the ANT group. Concentrations of acetate, propionate, butyrate, valerate, and isovalerate in GML2 were significantly higher (P < 0.05) than those in the NCO group on day 28. However, acetate, propionate, valerate, and isovalerate concentrations were reduced to significantly (P < 0.05) lower than those in the NCO group on day 56. The abundance and diversity of microbiota were found to be improved in broilers that were supplemented with GML, using operational taxonomic unit and diversity analyses. Furthermore, the GML treatments increased favorable microbiota, particularly acid-producing bacteria, on day 28 and, also, reduced opportunistic pathogens, such as Alistipes tidjanibacter and Bacteroides dorei by day 56. These results suggest that α-GML supplementation modulates cecal microbiota and broiler immunity and improves volatile fatty acid levels during the early growth stages of broilers.

Metabolic Analysis of Regionally Distinct Gut Microbial Communities Using an In Vitro Platform

The colon gut microbiota is responsible for complex chemical conversions of nutrients and subsequent release of metabolites that have diverse biological consequences. However, information on the metabolic dynamics that occur longitudinally through the colon is limited. Here, gas and liquid chromatographies coupled with mass spectrometry were applied to generate metabolic profiles of the region-specific microbial communities cultured using an in vitro platform simulating the ascending (AC), transverse (TC), and descending (DC) colon regions. Comparative analysis revealed a large divergence between metabolic profiles of the AC and the TC and DC regions in terms of short-chain fatty acid production, metabolic spectrum, and conversion of bile acids. Metagenomic evaluation revealed that the regionally derived metabolic profiles had strong correlation to community composition and genetic potential. Together, the results provide key insights regarding the metabolic divergence of the regional communities that are integral to understand the structure-function relationship of the gut microbiota.

Unravelling lactate-acetate and sugar conversion into butyrate by intestinal Anaerobutyricum and Anaerostipes species by comparative proteogenomics

The d- and l-forms of lactate are important fermentation metabolites produced by intestinal bacteria but are found to negatively affect mucosal barrier function and human health. Both enantiomers of lactate can be converted with acetate into the presumed beneficial butyrate by a phylogenetically related group of anaerobes, including Anaerobutyricum and Anaerostipes spp. This is a low energy yielding process with a partially unknown pathway in Anaerobutyricum and Anaerostipes spp. and hence, we sought to address this via a comparative genomics, proteomics and physiology approach. We compared growth of Anaerobutyricum soehngenii on lactate with that on sucrose and sorbitol. Comparative proteomics revealed complete pathway of butyrate formation from sucrose, sorbitol and lactate. Notably, a gene cluster, lctABCDEF was abundantly expressed when grown on lactate. This gene cluster encodes a lactate dehydrogenase (lctD), electron transport proteins A and B (lctCB), nickel-dependent racemase (lctE), lactate permease (lctF) and short-chain acyl-CoA dehydrogenase (lctG). Investigation of available genomes of intestinal bacteria revealed this new gene cluster to be highly conserved in only Anaerobutyricum and Anaerostipes spp. Present study demonstrates that A. soehngenii and several related Anaerobutyricum and Anaerostipes spp. are highly adapted for a lifestyle involving lactate plus acetate utilization in the human intestinal tract.

Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 12: suitability of taxonomic units notified to EFSA until March 2020

The qualified presumption of safety (QPS) was developed to provide a generic safety evaluation for biological agents to support EFSA's Scientific Panels. It is based on an assessment of the taxonomic identity, the body of knowledge, safety concerns and antimicrobial resistance. Safety concerns identified for a taxonomic unit (TU) are where possible to be confirmed at strain or product level, reflected by 'qualifications'. No new information was found that would change the previously recommended QPS TUs of the 39 microorganisms notified to EFSA between October 2019 and March 2020, 33 were excluded, including five filamentous fungi, five Escherichia coli, two Enterococcus faecium, two Streptomyces spp. and 19 TUs already evaluated. Six TUs were evaluated. Akkermansia muciniphila was not recommended for QPS status due to safety concerns. Clostridium butyricum was not recommended because some strains contain pathogenicity factors. This TU was excluded for further QPS evaluation. Galdieria sulphuraria and Pseudomonas chlororaphis were also rejected due to a lack of body of knowledge. The QPS status of Corynebacterium ammoniagenes (with the qualification 'for production purposes only') and of Komagataella pastoris (with the qualification 'for enzyme production') was confirmed. In relation to the taxonomic revision of the Lactobacillus genus, previously designated Lactobacillus species will be reassigned to the new species and both the old and new names will be retained in the QPS list.

Three-stage process for tequila vinasse valorization through sequential lactate, biohydrogen and methane production

This study evaluated a novel three-stage process devoted to the cascade production of lactate, biohydrogen and methane from tequila vinasse (TV), with emphasis on attaining a high and stable biohydrogen production rate (HPR) by utilizing lactate as biohydrogen precursor. In the first stage, tailored operating conditions applied to a sequencing batch reactor were effective in sustaining a lactate concentration of 12.4 g/L, corresponding to 89% of the total organic acids produced. In the second stage, the stimulation of lactate-centered dark fermentation which entails the decoupling of biohydrogen production from carbohydrates utilization was an effective approach enabling stable biohydrogen production, having HPR fluctuations less than 10% with a maximum HPR of 12.3 L/L-d and a biohydrogen yield of 3.1 L/L_TV. Finally, 1.6 L CH₄/L-d and 6.5 L CH₄/L_TV were obtained when feeding the biohydrogen fermentation effluent to a third methanogenic stage, yielding a global energy recovery of 267.5 kJ/L_TV.

Aerobic acetone-butanol-isopropanol (ABI) fermentation through a co-culture of Clostridium beijerinckii G117 and recombinant Bacillus subtilis 1A1

An engineered B. subtilis 1A1 strain (BsADH2) expressing a secondary alcohol dehydrogenase (CpSADH) was co-cultured with C. beijerinckii G117 under an aerobic condition. During the fermentation on glucose, B. subtilis BsADH2 depleted oxygen in culture media completely and created an anaerobic environment for C. beijerinckii G117, an obligate anaerobe, to grow. Meanwhile, lactate produced by B. subtilis BsADH2 was re-assimilated by C. beijerinckii G117. In return, acetone produced by C. beijerinckii G117 was reduced into isopropanol by B. subtilis BsADH2 via expressing the CpSADH, which helped maintain the redox balance of the engineered B. subtilis. In the symbiotic system consisting of two strains, 1.7 ​g/L of acetone, 4.8 ​g/L of butanol, and 0.9 ​g/L of isopropanol (with an isopropanol/acetone ratio of 0.53) was produced from 60 ​g/L of glucose. This symbiotic system also worked when oxygen was supplied to the culture, although less isopropanol was produced (0.9 ​g/L of acetone, 4.9 ​g/L of butanol, and 0.2 ​g/L of isopropanol). The isopropanol titer was increased substantially to 2.5 ​g/L when we increased the inoculum size of B. subtilis BsADH2 and optimized other process parameters. With the Bacillus-Clostridium co-culture, switching from the original acetone-butanol (AB) fermentation to an aerobic acetone-butanol-isopropanol (ABI) fermentation can be easily achieved without genetic engineering of Clostridium. This strategy of employing a recombinant Bacillus to co-culture with Clostridium should be potentially useful to modify traditional acetone-butanol-ethanol fermentation for the production of other value-added chemicals.

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A secondary alcohol dehydrogenase was expressed in Bacillus subtilis.

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Acetone-butanol was upgraded into acetone-butanol-isopropanol by B. subtilis.

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A mutualistic relationship was established between B. subtilis and C. beijerinckii.

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Aerobic co-culture of B. subtilis and C. beijerinckii was achieved.

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Clostridium fermentation was improved by introducing a genetically-modified strain.

Dysbiosis characteristics of gut microbiota in cerebral infarction patients

Objective

The aim of this study is to investigate the dysbiosis characteristics of gut microbiota in patients with cerebral infarction (CI) and its clinical implications.

Methods

Stool samples were collected from 79 CI patients and 98 healthy controls and subjected to 16S rRNA sequencing to identify stool microbes. Altered compositions and functions of gut microbiota in CI and its correlation with clinical features were investigated. Random forest and receiver operating characteristic analysis were used to develop a diagnostic model.

Results

Microbiota diversity and structure between CI patients and healthy controls were overall similar. However, butyrate-producing bacteria (BPB) were significantly reduced in CI patients, while lactic acid bacteria (LAB) were increased. Genetically, BPB-related functional genes were reduced in CI patients, whereas LAB-related genes were enhanced. The interbacterial correlations among BPB in CI patients were less prominent than those in healthy controls. Clinically, BPB was negatively associated with the National Institutes of Health Stroke Scale (NIHSS), while LAB was positively correlated with NIHSS. Both BPB and LAB played leading roles in the diagnostic model based on 47 bacteria.

Conclusions

The abundance and functions of BPB in CI patients were significantly decreased, while LAB were increased. Both BPB and LAB displayed promising potential in the assessment and diagnosis of CI.

Dynamics of Clostridium genus and hard-cheese spoiling Clostridium species in anaerobic digesters treating agricultural biomass

Biogas plants are a widespread renewable energy technology. However, the use of digestate for agronomic purposes has often been a matter of concern. It is controversial whether biogas plants might harbor some pathogenic clostridial species, which represent a biological risk. Moreover, the inhabitance of Clostridium hard-cheese spoiling species in anaerobic digesters can be problematic for hard-cheese manufacturing industries, due to the issue of cheese blowing defects. This study investigated the effect of mesophilic anaerobic digestion processes on the Clostridium consortia distribution over time. Specifically, three lab-scale CSTRs treating agricultural biomass were characterized by considering both the whole microbial community and the cultivable clostridial spores. It is assessed an overall reduction of the Clostridium genus during the anaerobic digestion process. Moreover, it was evidenced a slight, but steady decrease of the cultivable clostridial spores, mainly represented by two pathogenic species, C. perfringens and C. bifermentans, and one hard-cheese spoiling species, C. butyricum. Thus, it is revealed an overall reduction of the clostridial population abundance after the mesophilic anaerobic digestion treatment of agricultural biomass.

Glucose fermentation with biochar amended consortium: Sequential fermentations

The aim of this work was to study sequential batch fermentation of glucose with a biological consortium amended with nine different biochars or with an activated carbon. The glucose fermentation was enhanced by carbon amendment, with activated carbon being more effective than biochars as cell carriers and electron conductors between functional species. The volatile fatty acid distributions were shifted in the consumption of the produced H₂ and CO₂. The types of biochars were irrelevant to glucose glycolysis and the subsequent H₂ and CO₂ consumption reactions. Biofilm growth affects the detailed mechanisms occurred in fermentation broth to the yielded volatile fatty acid distributions.

Metabolomics reveals impact of seven functional foods on metabolic pathways in a gut microbiota model

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Metabolomics was employed to assess 7 functional foods impact on gut microbiota.

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Insights regarding how functional foods alter gut metabolic pathways is presented.

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Increased GABA production was observed in polyphenol rich functional food.

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Purine alkaloids served as direct substrate in microbiota metabolism.

Functional food defined as dietary supplements that in addition to their nutritional values, can beneficially modulate body functions becomes more and more popular but the reaction of the intestinal microbiota to it is largely unknown. In order to analyse the impact of functional food on the microbiota itself it is necessary to focus on the physiology of the microbiota, which can be assessed in a whole by untargeted metabolomics. Obtaining a detailed description of the gut microbiota reaction to food ingredients can be a key to understand how these organisms regulate and bioprocess many of these food components. Extracts prepared from seven chief functional foods, namely green tea, black tea, Opuntia ficus-indica (prickly pear, cactus pear), black coffee, green coffee, pomegranate, and sumac were administered to a gut consortium culture encompassing 8 microbes which are resembling, to a large extent, the metabolic activities found in the human gut. Samples were harvested at 0.5 and 24 h post addition of functional food extract and from blank culture in parallel and analysed for its metabolites composition using gas chromatography coupled to mass spectrometry detection (GC-MS). A total of 131 metabolites were identified belonging to organic acids, alcohols, amino acids, fatty acids, inorganic compounds, nitrogenous compounds, nucleic acids, phenolics, steroids and sugars, with amino acids as the most abundant class in cultures. Considering the complexity of such datasets, multivariate data analyses were employed to classify samples and investigate how functional foods influence gut microbiota metabolisms. Results from this study provided a first insights regarding how functional foods alter gut metabolism through either induction or inhibition of certain metabolic pathways, i.e. GABA production in the presence of higher acidity induced by functional food metabolites such as polyphenols. Likewise, functional food metabolites i.e., purine alkaloids acted themselves as direct substrate in microbiota metabolism.

Developing a Microbial Consortium for Enhanced Metabolite Production from Simulated Food Waste

Food waste disposal and transportation of commodity chemicals to the point-of-need are substantial challenges in military environments. Here, we propose addressing these challenges via the design of a microbial consortium for the fermentation of food waste to hydrogen. First, we simulated the exchange metabolic fluxes of monocultures and pairwise co-cultures using genome-scale metabolic models on a food waste proxy. We identified that one of the top hydrogen producing co-cultures comprised Clostridium beijerinckii NCIMB 8052 and Yokenella regensburgei ATCC 43003. A consortium of these two strains produced a similar amount of hydrogen gas and increased butyrate compared to the C. beijerinckii monoculture, when grown on an artificial garbage slurry. Increased butyrate production in the consortium can be attributed to cross-feeding of lactate produced by Y. regensburgei. Moreover, exogenous lactate promotes the growth of C. beijerinckii with or without a limited amount of glucose. Increasing the scale of the consortium fermentation proved challenging, as two distinct attempts to scale-up the enhanced butyrate production resulted in different metabolic profiles than observed in smaller scale fermentations. Though the genome-scale metabolic model simulations provided a useful starting point for the design of microbial consortia to generate value-added products from waste materials, further model refinements based on experimental results are required for more robust predictions.

Species Deletions from Microbiome Consortia Reveal Key Metabolic Interactions between Gut Microbes

The gut microbiome is a complex microbial community that plays a key role in human health. Diet is an important factor dictating gut microbiome composition. This is mediated by multiple microbe-microbe interactions that result in the fermentation of nondigestible carbohydrates and the production of short-chain fatty acids. Certain species play key metabolic roles in the microbiome, and their disappearance could result in dysbiosis. In this work, a synthetic consortium of 14 gut microbes was studied during the utilization of prebiotic inulin in batch bioreactors. Fermentations were repeated leaving one species out every time, in order to evaluate the impact of their elimination on the system. Substrate consumption, microbial composition, and metabolite production were determined. Single deletions never resulted in a complete loss of bacterial growth or inulin consumption, suggesting functional redundancy. Deletions of Bacteroides dorei and Lachnoclostridium clostridioforme resulted in lower biomass and higher residual inulin. The absence of B. dorei impacted the abundance of the other 10 species negatively. Lachnoclostridium symbiosum, a butyrate producer, appeared to be the most sensitive species to deletions, being stimulated by the presence of Escherichia coli, Bifidobacterium adolescentis, B. dorei, and Lactobacillus plantarum Conversely, bioreactors without these species did not show butyrate production. L. clostridioforme was observed to be essential for propionate production, and B. dorei for lactate production. Our analysis identified specific members that were essential for the function of the consortium. In conclusion, species deletions from microbial consortia could be a useful approach to identify relevant interactions between microorganisms and defining metabolic roles in the gut microbiome.IMPORTANCE Gut microbes associate, compete for, and specialize in specific metabolic tasks. These interactions are dictated by the cross-feeding of degradation or fermentation products. However, the individual contribution of microbes to the function of the gut microbiome is difficult to evaluate. It is essential to understand the complexity of microbial interactions and how the presence or absence of specific microorganisms affects the stability and functioning of the gut microbiome. The experimental approach of this study could be used for identifying keystone species, in addition to redundant functions and conditions that contribute to community stability. Redundancy is an important feature of the microbiome, and its reduction could be useful for the design of microbial consortia with desired metabolic properties enhancing the tasks of the keystone species.

Key sub-community dynamics of medium-chain carboxylate production

BACKGROUND

The carboxylate platform is a promising technology for substituting petrochemicals in the provision of specific platform chemicals and liquid fuels. It includes the chain elongation process that exploits reverse β-oxidation to elongate short-chain fatty acids and forms the more valuable medium-chain variants. The pH value influences this process through multiple mechanisms and is central to effective product formation. Its influence on the microbiome dynamics was investigated during anaerobic fermentation of maize silage by combining flow cytometric short interval monitoring, cell sorting and 16S rRNA gene amplicon sequencing.

RESULTS

Caproate and caprylate titres of up to 6.12 g L-1 and 1.83 g L-1, respectively, were achieved in a continuous stirred-tank reactor operated for 241 days. Caproate production was optimal at pH 5.5 and connected to lactate-based chain elongation, while caprylate production was optimal at pH 6.25 and linked to ethanol utilisation. Flow cytometry recorded 31 sub-communities with cell abundances varying over 89 time points. It revealed a highly dynamic community, whereas the sequencing analysis displayed a mostly unchanged core community. Eight key sub-communities were linked to caproate or caprylate production (rS > | ± 0.7|). Amongst other insights, sorting and subsequently sequencing these sub-communities revealed the central role of Bifidobacterium and Olsenella, two genera of lactic acid bacteria that drove chain elongation by providing additional lactate, serving as electron donor.

CONCLUSIONS

High-titre medium-chain fatty acid production in a well-established reactor design is possible using complex substrate without the addition of external electron donors. This will greatly ease scaling and profitable implementation of the process. The pH value influenced the substrate utilisation and product spectrum by shaping the microbial community. Flow cytometric single cell analysis enabled fast, short interval analysis of this community and was coupled with 16S rRNA gene amplicon sequencing to reveal the major role of lactate-producing bacteria.