Selecting for lactic acid producing and utilising bacteria in anaerobic enrichment cultures

Bacteria colonization and gene expression related to immune function in colon mucosa is associated with growth in neonatal calves regardless of live yeast supplementation

BACKGROUND

As Holstein calves are susceptible to gastrointestinal disorders during the first week of life, understanding how intestinal immune function develops in neonatal calves is important to promote better intestinal health. Feeding probiotics in early life may contribute to host intestinal health by facilitating beneficial bacteria colonization and developing intestinal immune function. The objective of this study was to characterize the impact of early life yeast supplementation and growth on colon mucosa-attached bacteria and host immune function.

RESULTS

Twenty Holstein bull calves received no supplementation (CON) or Saccharomyces cerevisiae boulardii (SCB) from birth to 5 d of life. Colon tissue biopsies were taken within 2 h of life (D0) before the first colostrum feeding and 3 h after the morning feeding at d 5 of age (D5) to analyze mucosa-attached bacteria and colon transcriptome. Metagenome sequencing showed that there was no difference in α and β diversity of mucosa-attached bacteria between day and treatment, but bacteria related to diarrhea were more abundant in the colon mucosa on D0 compared to D5. In addition, qPCR indicated that the absolute abundance of Escherichia coli (E. coli) decreased in the colon mucosa on D5 compared to D0; however, that of Bifidobacterium, Lactobacillus, and Faecalibacterium prausnitzii, which could competitively exclude E. coli, increased in the colon mucosa on D5 compared to D0. RNA-sequencing showed that there were no differentially expressed genes between CON and SCB, but suggested that pathways related to viral infection such as "Interferon Signaling" were activated in the colon mucosa of D5 compared to D0.

CONCLUSIONS

Growth affected mucosa-attached bacteria and host immune function in the colon mucosa during the first 5 d of life in dairy calves independently of SCB supplementation. During early life, opportunistic pathogens may decrease due to intestinal environmental changes by beneficial bacteria and/or host immune function. Predicted activation of immune function-related pathways may be the result of host immune function development or suggest other antigens in the intestine during early life. Further studies focusing on the other antigens and host immune function in the colon mucosa are required to better understand intestinal immune function development.

Microbiome-functionality in anaerobic digesters: A critical review

Microbially driven anaerobic digestion (AD) processes are of immense interest due to their role in the biovalorization of biowastes into renewable energy resources. The function-versatile microbiome, interspecies syntrophic interactions, and trophic-level metabolic pathways are important microbial components of AD. However, the lack of a comprehensive understanding of the process hampers efforts to improve AD efficiency. This study presents a holistic review of research on the microbial and metabolic "black box" of AD processes. Recent research on microbiology, functional traits, and metabolic pathways in AD, as well as the responses of functional microbiota and metabolic capabilities to optimization strategies are reviewed. The diverse ecophysiological traits and cooperation/competition interactions of the functional guilds and the biomanipulation of microbial ecology to generate valuable products other than methane during AD are outlined. The results show that AD communities prioritize cooperation to improve functional redundancy, and the dominance of specific microbes can be explained by thermodynamics, resource allocation models, and metabolic division of labor during cross-feeding. In addition, the multi-omics approaches used to decipher the ecological principles of AD consortia are summarized in detail. Lastly, future microbial research and engineering applications of AD are proposed. This review presents an in-depth understanding of microbiome-functionality mechanisms of AD and provides critical guidance for the directional and efficient bioconversion of biowastes into methane and other valuable products.

Why do lactic acid bacteria thrive in chain elongation microbiomes?

Efficient waste management is necessary to transition towards a more sustainable society. An emerging trend is to use mixed culture biotechnology to produce chemicals from organic waste. Insights into the metabolic interactions between community members and their growth characterization are needed to mediate knowledge-driven bioprocess development and optimization. Here, a granular sludge bioprocess for the production of caproic acid through sugar-based chain elongation metabolism was established. Lactic acid and chain-elongating bacteria were identified as the two main functional guilds in the granular community. The growth features of the main community representatives (isolate Limosilactobacillus musocae G03 for lactic acid bacteria and type strain Caproiciproducens lactatifermentans for chain-elongating bacteria) were characterized. The measured growth rates of lactic acid bacteria (0.051 ± 0.005 h-1) were two times higher than those of chain-elongating bacteria (0.026 ± 0.004 h-1), while the biomass yields of lactic acid bacteria (0.120 ± 0.005 g biomass/g glucose) were two times lower than that of chain-elongating bacteria (0.239 ± 0.007 g biomass/g glucose). This points towards differential growth strategies, with lactic acid bacteria resembling that of a r-strategist and chain-elongating bacteria resembling that of a K-strategist. Furthermore, the half-saturation constant of glucose for L. mucosae was determined to be 0.35 ± 0.05 g/L of glucose. A linear trend of caproic acid inhibition on the growth of L. mucosae was observed, and the growth inhibitory caproic acid concentration was predicted to be 13.6 ± 0.5 g/L, which is the highest reported so far. The pre-adjustment of L. mucosae to 4 g/L of caproic acid did not improve the overall resistance to it, but did restore the growth rates at low caproic acid concentrations (1-4 g/L) to the baseline values (i.e., growth rate at 0 g/L of caproic acid). High resistance to caproic acid enables lactic acid bacteria to persist and thrive in the systems intended for caproic acid production. Here, insights into the growth of two main functional guilds of sugar-based chain elongation systems are provided which allows for a better understanding of their interactions and promotes future bioprocess design and optimization.

Aerobic granular sludge phosphate removal using glucose

Enhanced biological phosphate removal and aerobic sludge granulation are commonly studied with fatty acids as substrate. Fermentative substrates such as glucose have received limited attention. In this work, glucose conversion by aerobic granular sludge and its impact on phosphate removal was studied. Long-term stable phosphate removal and successful granulation were achieved. Glucose was rapidly taken up (273 mg/gVSS/h) at the start of the anaerobic phase, while phosphate was released during the full anaerobic phase. Some lactate was produced during glucose consumption, which was anaerobically consumed once glucose was depleted. The phosphate release appeared to be directly proportional to the uptake of lactate. The ratio of phosphorus released to glucose carbon taken up over the full anaerobic phase was 0.25 Pmol/Cmol. Along with glucose and lactate uptake in the anaerobic phase, poly‑hydroxy-alkanoates and glycogen storage were observed. There was a linear correlation between glucose consumption and lactate formation. While lactate accounted for approximately 89 % of the observed products in the bulk liquid, minor quantities of formate (5 %), propionate (4 %), and acetate (3 %) were also detected (mass fraction). Formate was not consumed anaerobically. Quantitative fluorescence in-situ hybridization (qFISH) revealed that polyphosphate accumulating organisms (PAO) accounted for 61 ± 15 % of the total biovolume. Metagenome evaluation of the biomass indicated a high abundance of Micropruina and Ca. Accumulibacter in the system, which was in accordance with the microscopic observations and the protein mass fraction from metaproteome analysis. Anaerobic conversions were evaluated based on theoretical ATP balances to provide the substrate distribution amongst the dominant genera. This research shows that aerobic granular sludge technology can be applied to glucose-containing effluents and that glucose is a suitable substrate for achieving phosphate removal. The results also show that for fermentable substrates a microbial community consisting of fermentative organisms and PAO develop.

Detection of extended-spectrum β-lactamase-producing Escherichia coli genes isolated from cat rectal swabs at Surabaya Veterinary Hospital, Indonesia

Background and Aim

Escherichia coli causes a bacterial illness that frequently affects cats. Diseases caused by E. coli are treated using antibiotics. Because of their proximity to humans, cats possess an extremely high risk of contracting antibiotic resistance genes when their owners touch cat feces containing E. coli that harbor resistance genes. This study was conducted to identify multidrug-resistant E. coli and extended-spectrum β-lactamase (ESBL)-producing genes from cat rectal swabs collected at Surabaya City Veterinary Hospital to determine antibiotic sensitivity.

Materials and Methods

Samples of cat rectal swabs were cultured in Brilliant Green Bile Lactose Broth medium and then streaked on eosin methylene blue agar medium for bacterial isolation, whereas Gram-staining and IMViC tests were conducted to confirm the identification results. The Kirby-Bauer diffusion test was used to determine antibiotic sensitivity, and the double-disk synergy test was used to determine ESBL-producing bacteria. Molecular detection of the genes TEM and CTX-M was performed using a polymerase chain reaction.

Results

Based on morphological culture, Gram-staining, and biochemical testing, the results of sample inspection showed that of the 100 cat rectal swab samples isolated, 71 (71%) were positive for E. coli. Furthermore, 23 E. coli isolates (32.39%) demonstrated the highest resistance to ampicillin. Four isolates were confirmed to be multidurg-resistant and ESBL-producing strains. Molecular examination revealed that three E. coli isolates harbored TEM and CTX-M.

Conclusion

In conclusion, pet owners must be educated on the use of antibiotics to improve their knowledge about the risks of antibiotic resistance.

Short-chain fatty acids (SCFAs) as potential resuscitation factors that promote the isolation and culture of uncultured bacteria in marine sediments

Many marine bacteria are difficult to culture because they are dormant, rare or found in low-abundances. Enrichment culturing has been widely tested as an important strategy to isolate rare or dormant microbes. However, many more mechanisms remain uncertain. Here, based on 16S rRNA gene high-throughput sequencing and metabolomics technology, it was found that the short-chain fatty acids (SCFAs) in metabolites were significantly correlated with uncultured bacterial groups during enrichment cultures. A pure culture analysis showed that the addition of SCFAs to media also resulted in high efficiency for the isolation of uncultured strains from marine sediments. As a result, 238 strains belonging to 10 phyla, 26 families and 82 species were successfully isolated. Some uncultured rare taxa within Chlorobi and Kiritimatiellaeota were successfully cultured. Amongst the newly isolated uncultured microbes, most genomes, e.g. bacteria, possess SCFA oxidative degradation genes, and these features might aid these microbes in better adapting to the culture media. A further resuscitation analysis of a viable but non-culturable (VBNC) Marinilabiliales strain verified that the addition of SCFAs could break the dormancy of Marinilabiliales in 5 days, and the growth curve test showed that the SCFAs could shorten the lag phase and increase the growth rate. Overall, this study provides new insights into SCFAs, which were first studied as resuscitation factors in uncultured marine bacteria. Thus, this study can help improve the utilisation and excavation of marine microbial resources, especially for the most-wanted or key players.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-023-00187-w.

Microbial Fermentation Processes of Lactic Acid: Challenges, Solutions, and Future Prospects

The demand for lactic acid and lactic acid-derived products in the food, pharmaceutical, and cosmetic industries is increasing year by year. In recent decades, the synthesis of lactic acid by microbials has gained much attention from scientists due to the superior optical purity of the product, its low production costs, and its higher production efficiency compared to chemical synthesis. Microbial fermentation involves the selection of feedstock, strains, and fermentation modes. Each step can potentially affect the yield and purity of the final product. Therefore, there are still many critical challenges in lactic acid production. The costs of feedstocks and energy; the inhibition of substrates and end-product; the sensitivity to the inhibitory compounds released during pretreatment; and the lower optical purity are the main obstacles hindering the fermentation of lactic acid. This review highlights the limitations and challenges of applying microbial fermentation in lactic acid production. In addition, corresponding solutions to these difficulties are summarized in order to provide some guidance for the industrial production of lactic acid.

Intestinal Production of Alpha-Glucosidase Inhibitor by Bacillus coagulans Spores

This study examines the possibility of directly producing and utilizing useful substances in the intestines of animals using anaerobic bacteria that can grow in the intestines of animals. A facultative anaerobe producing a large amount of α-glucosidase inhibitor was isolated from hay and identified and named Bacillus coagulans CC. The main compound of α-glucosidase inhibitor produced by Bacillus coagulans CC was identified as 1-deoxynojirimycin. α-glucosidase inhibitor activity was confirmed in the intestinal contents and feces of mice orally administered with spores of this strain, and it was confirmed that this strain could efficiently reach the intestines, proliferate, and produce α-glucosidase inhibitors. As a result of administering Bacillus coagulans CC to mice at 10⁹ cells per 1 kg body weight of spores for 8 weeks, the high-carbohydrate diet and the high-fat diet showed a 5% lower weight gain compared to the non-administrated group. At this point, in the spore-administered group, a decrease was observed in both the visceral and subcutaneous fat layers of the abdomen and thorax in both high-carbohydrate and high-fat diet groups compared to the non-administered group on computed tomography. The results of this study show that α-glucosidase inhibitors produced in the intestine by specific strains can work efficiently.

Limosilactobacillus fermentum, Lactococcus lactis and Thomasclavelia ramosa are enriched and Methanobrevibacter smithii is depleted in patients with non-alcoholic steatohepatitis

Non-alcoholic fatty liver (NAFLD), and its complicated form, non-alcoholic steatohepatitis (NASH), have been associated with gut dysbiosis with specific signatures. Endogenous ethanol production by Klebsiella pneumoniae or yeasts has been identified as a potential physio-pathological mechanism. A species-specific association between Lactobacillus and obesity and metabolic diseases has been reported. In this study, the microbial composition of ten cases of NASH and ten controls was determined using v3v4 16S amplicon sequencing as well as quantitative PCR (qPCR). Using different statistical approaches, we found an association of Lactobacillus and Lactoccocus with NASH, and an association of Methanobrevibacter, Faecalibacterium and Romboutsia with controls. At the species level, Limosilactobacillus fermentum and Lactococcus lactis, two species producing ethanol, and Thomasclavelia ramosa, a species already associated with dysbiosis, were associated with NASH. Using qPCR, we observed a decreased frequency of Methanobrevibacter smithii and confirmed the high prevalence of L. fermentum in NASH samples (5/10), while all control samples were negative (p = 0.02). In contrast, Ligilactobacillus ruminis was associated with controls. This supports the critical importance of taxonomic resolution at the species level, notably with the recent taxonomic reclassification of the Lactobacillus genus. Our results point towards the potential instrumental role of ethanol-producing gut microbes in NASH patients, notably lactic acid bacteria, opening new avenues for prevention and treatment.

Model-aided targeted volatile fatty acid production from food waste using a defined co-culture microbial community

The production of volatile fatty acids (VFA) is gaining momentum due to their central role in the emerging carboxylate platform. Particularly, the production of the longest VFA (from butyrate to caproate) is desired due to their increased economic value and easier downstream processing. While the use of undefined microbial cultures is usually preferred with organic waste streams, the use of defined microbial co-culture processes could tackle some of their drawbacks such as poor control over the process outcome, which often leads to low selectivity for the desired products. However, the extensive experimentation needed to design a co-culture system hinders the use of this technology. In this work, a workflow based on the combined use of mathematical models and wet experimentation is proposed to accelerate the design of novel bioprocesses. In particular, a co-culture consisting of Pediococcus pentosaceus and Megaphaera cerevisiae is used to target the production of high-value odd- and even‑carbon VFA. An unstructured kinetic model was developed, calibrated and used to design experiments with the goal of increasing the selectivity for the desired VFA, which were experimentally validated. In the case of even‑carbon VFA, the experimental validation showed an increase of 38 % in caproate yield and, in the case of enhanced odd‑carbon VFA experiments, the yield of butyrate and caproate diminished by 62 % and 94 %, respectively, while propionate became one of the main end products and valerate yield value increased from 0.007 to 0.085 g_valearte per g_{consumed sugar.} The workflow followed in this work proved to be a sound tool for bioprocess design due to its capacity to explore and design new experiments in silico in a fast way and ability to quickly adapt to new scenarios.

Recent Progress in Electronic Noses for Fermented Foods and Beverages Applications

Fermented foods and beverages have become a part of daily diets in several societies around the world. Emitted volatile organic compounds play an important role in the determination of the chemical composition and other information of fermented foods and beverages. Electronic nose (E-nose) technologies enable non-destructive measurement and fast analysis, have low operating costs and simplicity, and have been employed for this purpose over the past decades. In this work, a comprehensive review of the recent progress in E-noses is presented according to the end products of the main fermentation types, including alcohol fermentation, lactic acid fermentation, acetic acid fermentation and alkaline fermentation. The benefits, research directions, limitations and challenges of current E-nose systems are investigated and highlighted for fermented foods and beverage applications.

Pre-incubation conditions determine the fermentation pattern and microbial community structure in fermenters at mild hydrostatic pressure

Fermentation at elevated hydrostatic pressure is a novel strategy targeting product selectivity. However, the role of inoculum history and cross-resistance, that is, acquired tolerance from incubation under distinctive environmental stress, remains unclear in high-pressure operation. In our here presented work, we studied fermentation and microbial community responses of halotolerant marine sediment inoculum (MSI) and anaerobic digester inoculum (ADI), pre-incubated in serum bottles at different temperatures and subsequently exposed to mild hydrostatic pressure (MHP; < 10 MPa) in stainless steel reactors. Results showed that MHP effects on microbial growth, activity, and community structure were strongly temperature-dependent. At moderate temperature (20°C), biomass yield and fermentation were not limited by MHP; suggesting a cross-resistance effect from incubation temperature and halotolerance. Low temperatures (10°C) and MHP imposed kinetic and bioenergetic limitations, constraining growth and product formation. Fermentation remained favorable in MSI at 28°C and ADI at 37°C, despite reduced biomass yield resulting from maintenance and decay proportionally increasing with temperature. Microbial community structure was modified by temperature during the enrichment, and slight differences observed after MHP-exposure did not compromise functionality. Results showed that the relation incubation temperature-halotolerance proved to be a modifier of microbial responses to MHP and could be potentially exploited in fermentations to modulate product/biomass ratio.

Enhanced fermentative lactic acid production from source-sorted organic household waste: Focusing on low-pH microbial adaptation and bio-augmentation strategy

Lactic acid (LA) production at low pH could significantly reduce the need for neutralizing agents, leading to reduction of operational costs. In the present study, LA production at acidic conditions was investigated using source-sorted organic household waste (SSOHW). Controlling the pH at low value (i.e. 5.0) and bio-augmenting with Pediococcus acidilactici led to a concentration of 39.3 ± 0.5 g_-LA/L with a yield of 0.75 ± 0.02 g_-LA/g_-sugar. In contrast, secondary fermentation at higher pH level (i.e. 5.5 and 6.0) resulted in complete LA degradation. Subsequently, consecutive batch fermentations were conducted to adapt P. acidilactici to SSOHW and improve the LA production. Results showed that P. acidilactici could successively adapt in the SSOHW reaching a relative abundance above 2.8% at adaptation process. The added P. acidilactici ensured a high concentration of LA at three consecutive generations, achieving an increment above 18% compared to control test (abiotic augmentation). Moreover, adaptation processes (i.e. maintaining pH at 4.0 or stepwise decreasing the pH from 5.0 to 4.0) significantly improved LA concentration and productivity at the pH of 4.0. Overall, the results provide a promising method to reduce the LA production costs using residual resources.

Biohydrogen production by mixed culture of Megasphaera elsdenii with lactic acid bacteria as Lactate-driven dark fermentation

Numerous attempts have been made to upscale biohydrogen production via dark fermentation (DF); however, the Achilles' heel of DF, i.e., lactic acid bacteria (LAB) contamination and overgrowth, hinders such upscaling. Key microbes are needed to develop a lactate-driven DF system that can serve as a lactate fermentation platform. In this study, the utility of Megasphaera elsdenii and LAB co-culturing in lactate-driven DF was evaluated. When inoculated simultaneously with LAB or after LAB culture, M. elsdenii achieved a stable hydrogen yield of 0.95-1.49 H₂-mol/mol-glucose, approximately half that obtained in pure M. elsdenii cultures. Hydrogen production was maintained even at an initial M. elsdenii-to-LAB cell ratio of one-millionth or less. Moreover, M. elsdenii produced hydrogen via lactate-driven DF from unusable sugars such as xylose or cellobiose. Thus, M. elsdenii could be a Game changer instrumental in unlocking the full potential of DF.

A preliminary study on a novel bioaugmentation technique enhancing lactic acid production by mixed cultures fermentation

The paper is a preliminary study on the selection of lactic acid producing microorganisms from a mixed microbial population via bioaugmentation. The bioaugmentation technique is based on pH sudden variations occurring in sequential batch steps of a dark fermentation process applied to simple substrates. Different conditions are tested and compared. The structure of microbial communities and concentrations of metabolic intermediates are analyzed to study the possible substrate conversion routes. Obtained results indicate that the initial mixed culture produced a lactic acid percentage of 5% in terms of COD_LA/COD_PRODUCTS. In the most favourable conditions, the selected culture produced a lactic acid percentage of 59%. The analysis of the composition of microbial communities before and after the bioaugmentation processes, indicates that lactic acid production mainly results from the population change to bacteria belonging to the genus Bacillus. Indeed, the relative abundance of Bacilli increased from 0.67%, to 8.40% during the bioaugmentation cycle.

Volatile Fatty Acid Production from Organic Waste with the Emphasis on Membrane-Based Recovery

In recent years, interest in the biorefinery concept has emerged in the utilization of volatile fatty acids (VFAs) produced by acidogenic fermentation as precursors for various biotechnological processes. This has attracted substantial attention to VFA production from low-cost substrates such as organic waste and membrane based VFA recovery techniques to achieve cost-effective and environmentally friendly processes. However, there are few reviews which emphasize the acidogenic fermentation of organic waste into VFAs, and VFA recovery. Therefore, this article comprehensively summarizes VFA production, the factors affecting VFA production, and VFA recovery strategies using membrane-based techniques. Additionally, the outlook for future research on VFA production is discussed.

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.

Product Inhibition and pH Affect Stoichiometry and Kinetics of Chain Elongating Microbial Communities in Sequencing Batch Bioreactors

Anaerobic microbial communities can produce carboxylic acids of medium chain length (e.g., caproate, caprylate) by elongating short chain fatty acids through reversed β-oxidation. Ethanol is a common electron donor for this process. The influence of environmental conditions on the stoichiometry and kinetics of ethanol-based chain elongation remains elusive. Here, a sequencing batch bioreactor setup with high-resolution off-gas measurements was used to identify the physiological characteristics of chain elongating microbial communities enriched on acetate and ethanol at pH 7.0 ± 0.2 and 5.5 ± 0.2. Operation at both pH-values led to the development of communities that were highly enriched (>50%, based on 16S rRNA gene amplicon sequencing) in Clostridium kluyveri related species. At both pH-values, stably performing cultures were characterized by incomplete substrate conversion and decreasing biomass-specific hydrogen production rates during an operational cycle. The process stoichiometries obtained at both pH-values were different: at pH 7.0, 71 ± 6% of the consumed electrons were converted to caproate, compared to only 30 ± 5% at pH 5.5. Operating at pH 5.5 led to a decrease in the biomass yield, but a significant increase in the biomass-specific substrate uptake rate, suggesting that the organisms employ catabolic overcapacity to deal with energy losses associated to product inhibition. These results highlight that chain elongating conversions rely on a delicate balance between substrate uptake- and product inhibition kinetics.

High-rate ethanol production at low pH using the anaerobic granular sludge process

In this study, we investigated the operational performance and product spectrum of glucose-fermenting anaerobic granular sludge reactor at pH 4. A selective environment for the growth of granules was implemented by the introduction of a 2 min settling phase, a hydraulic retention time of 6 h and a solid retention time of 12 ± 3 days. The fermentation products were ethanol, lactate, and volatile fatty acids (VFA) with yields of 0.55 ± 0.03, 0.15 ± 0.02, and 0.20 ± 0.04 gram chemical oxygen demand (gCOD)/gCOD glucose, respectively. The obtained product spectrum was remarkably different from the VFA-dominated product spectrum reported in a previous study when the same system was operated at higher pH (4.5-5.5). The shift in product spectrum coincided with a shift in the microbial community structure with the dominance of eukaryotic Candida tropicalis, Pichia jaroonii, and prokaryotic Lactobacillus species instead of the Clostridia species obtained at higher pH-values. The control of the microbiomes and the associated product spectra provides bioprocess engineers with the option to tailor a suitable precursor compound mixture for subsequent chain elongation fermentation or PHA biopolymer production.

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.

Directing carbohydrates toward ethanol using mesophilic microbial communities

Bioethanol production is an established biotechnological process. Margins are low which prevent a larger scale production of bioethanol. As a large part of the production cost is due to the feedstock, the use of low value unsterile feedstocks fermented by microbial communities will enable a more cost-competitive bioethanol production. To select for high yield ethanol producing communities, three selective conditions are proposed: acid washing of the cells after fermentation, a low pH (<5) during the fermentation and microaerobiosis at the start of the fermentation. Ethanol producers, such as Zymomonas species and yeasts, compete for carbohydrates with volatile fatty acid and lactic acid producing bacteria. Creating effective consortia of lactic acid bacteria and homo-ethanol producers at low pH will lead to robust and competitive ethanol yields and titres. A conceptual design of an ecology-based bioethanol production process is proposed using food waste to produce bioethanol, electricity, digestate and heat.

Microbial inefficient substrate use through the perspective of resource allocation models

Microorganisms extract energy from substrates following strategies that may seem suboptimal at first glance. Beyond the so-called yield-rate trade-off, resource allocation models, which focus on assigning different functional roles to the limited number of enzymes that a cell can support, offer a framework to interpret the inefficient substrate use by microorganisms. We review here relevant examples of substrate conversions where a significant part of the available energy is not utilised and how resource allocation models offer a mechanistic interpretation thereof, notably for open mixed cultures. Future developments are identified, in particular, the challenge of considering metabolic flexibility towards uncertain environmental changes instead of strict fixed optimality objectives, with the final goal of increasing the prediction capabilities of resource allocation models. Finally, we highlight the relevance of resource allocation to understand and enable a promising biorefinery platform revolving around lactate, which would increase the flexibility of waste-to-chemical biorefinery schemes.

A framework based on fundamental biochemical principles to engineer microbial community dynamics

Microbial communities are complex but there are basic principles we can apply to constrain the assumed stochasticity of their activity. By understanding the trade-offs behind the kinetic parameters that define microbial growth, we can explain how local interspecies dependencies arise and shape the emerging properties of a community. If we integrate these theoretical descriptions with experimental 'omics' data and bioenergetics analysis of specific environmental conditions, predictions on activity, assembly and spatial structure can be obtained reducing the a priori unpredictable complexity of microbial communities. This information can be used to define the appropriate selective pressures to engineer bioprocesses and propose new hypotheses which can drive experimental research to accelerate innovation in biotechnology.

Variation of Gut Microbiome in Free-Ranging Female Tibetan Macaques (Macaca thibetana) across Different Reproductive States

The gut microbiome is expected to adapt to the varying energetic and nutritional pressures in females of different reproductive states. Changes in the gut microbiome may lead to varying nutrient utilizing efficiency in pregnant and lactating female primates. In this study, we examined variation in the gut bacterial community composition of wild female Tibetan macaques (Macaca thibetana) across different reproductive states (cycling, pregnancy and lactation). Fecal samples (n = 25) were collected from ten adult females harvested across different reproductive states. Gut microbial community composition and potential functions were assessed using 16 S rRNA gene sequences. We found significant changes in gut bacterial taxonomic composition, structure and their potential functions in different reproductive states of our study species. In particular, the relative abundance of Proteobacteria increased significantly during pregnancy and lactation. In addition, the relative abundance of Succinivibrionaceae and Succinivibrio (Succinivibrionaceae) were overrepresented in pregnant females, whereas Bifidobacteriaceae and Bifidobacterium (Bifidobacteriaceae) were overrepresented in lactating females. Furthermore, the relative abundance of predicted functional genes of several metabolic pathways related to host's energy and nutrition, such as metabolism of carbohydrates, cofactors and vitamins, glycans and other amino acids, were enriched in pregnancy and lactation. Our findings suggest that changes in the gut microbiome may play an important role in meeting the energetic needs of pregnant and lactating Tibetan macaques. Future studies of the "microbial reproductive ecology" of primates that incorporate food availability, reproductive seasonality, female reproductive physiology and gut inflammation are warranted.

Resource allocation explains lactic acid production in mixed-culture anaerobic fermentations

Lactate production in anaerobic carbohydrate fermentations with mixed cultures of microorganisms is generally observed only in very specific conditions: the reactor should be run discontinuously and peptides and B vitamins must be present in the culture medium as lactic acid bacteria (LAB) are typically auxotrophic for amino acids. State-of-the-art anaerobic fermentation models assume that microorganisms optimise the adenosine triphosphate (ATP) yield on substrate and therefore they do not predict the less ATP efficient lactate production, which limits their application for designing lactate production in mixed-culture fermentations. In this study, a metabolic model taking into account cellular resource allocation and limitation is proposed to predict and analyse under which conditions lactate production from glucose can be beneficial for microorganisms. The model uses a flux balances analysis approach incorporating additional constraints from the resource allocation theory and simulates glucose fermentation in a continuous reactor. This approach predicts lactate production is predicted at high dilution rates, provided that amino acids are in the culture medium. In minimal medium and lower dilution rates, mostly butyrate and no lactate is predicted. Auxotrophy for amino acids of LAB is identified to provide a competitive advantage in rich media because less resources need to be allocated for anabolic machinery and higher specific growth rates can be achieved. The Matlab™ codes required for performing the simulations presented in this study are available at https://doi.org/10.5281/zenodo.4031144.

Selecting for lactic acid producing and utilising bacteria in anaerobic enrichment cultures

Lactic acid‐producing bacteria are important in many fermentations, such as the production of biobased plastics. Insight in the competitive advantage of lactic acid bacteria over other fermentative bacteria in a mixed culture enables ecology‐based process design and can aid the development of sustainable and energy‐efficient bioprocesses. Here we demonstrate the enrichment of lactic acid bacteria in a controlled sequencing batch bioreactor environment using a glucose‐based medium supplemented with peptides and B vitamins. A mineral medium enrichment operated in parallel was dominated by Ethanoligenens species and fermented glucose to acetate, butyrate and hydrogen. The complex medium enrichment was populated by Lactococcus, Lactobacillus and Megasphaera species and showed a product spectrum of acetate, ethanol, propionate, butyrate and valerate. An intermediate peak of lactate was observed, showing the simultaneous production and consumption of lactate, which is of concern for lactic acid production purposes. This study underlines that the competitive advantage for lactic acid‐producing bacteria primarily lies in their ability to attain a high biomass specific uptake rate of glucose, which was two times higher for the complex medium enrichment when compared to the mineral medium enrichment. The competitive advantage of lactic acid production in rich media can be explained using a resource allocation theory for microbial growth processes.