Two-species community design of lactic acid bacteria for optimal production of lactate

Harnessing microbial division of labor for biomanufacturing: a review of laboratory and formal modeling approaches

Bioprocess industries aim to meet the increasing demand for product complexity by designing enhanced cellular and metabolic capabilities for the host. Monocultures, standard biomanufacturing workhorses, are often restricted in their capability to meet these demands, and the solution often involves the genetic modification of the host. Synthetic microbial communities are a promising alternative to monocultures because they exhibit division of labor, enabling efficient resource utilization and pathway modularity. This specialization minimizes metabolic burden and enhances robustness to perturbations, providing a competitive advantage. Despite this potential, their utilization in biotechnological or bioprocessing applications remains limited. The recent emergence of new and innovative community design tools and strategies, particularly those harnessing the division of labor, holds promise to change this outlook. Understanding the microbial interactions governing natural microbial communities can be used to identify complementary partners, informing synthetic community design. Therefore, we particularly consider engineering division of labor in synthetic microbial communities as a viable solution to accelerate progress in the field. This review presents the current understanding of how microbial interactions enable division of labor and how this information can be used to design synthetic microbial communities to perform tasks otherwise unfeasible to individual organisms. We then evaluate laboratory and formal modeling approaches specifically developed to: elucidate microbial community physiology, guide experimental design, and improve our understanding of complex community interactions assisting synthetic community design. By synthesizing these insights, we aim to present a comprehensive framework that advances the use of microbial communities in biomanufacturing applications.

Multiphasic and mixture lactic acid bacteria screening approach for the removal of antinutrients and off-flavors present in a pea, oat and potato blend

The antinutrients and off-flavors present in plant-based foods are some of the major organoleptic and consumer acceptance drawbacks considered when developing plant-based fermented dairy alternatives (PBFDA). Here, we investigated a combination of genotypical and phenotypical consecutive screening methods to find out the optimal single- and combination of lactic acid bacteria (LAB) strains based on volatile off-flavors, phenolic acids, saponins, and trypsin inhibitor degradation through the fermentation of a pea, oat, and potato (POP) blend. Lactiplantibacillus plantarum strains were the most optimal for the partial/complete degradation of p-coumaric (>98 %) and ferulic acid (10-20 %) compounds in the POP blend. Leuconostoc pseudomesenteroides strains, and their PII-type proteinases were demonstrated to be effective degrading trypsin inhibitors. Also, specific Leuconostoc mesenteroides and L. plantarum strains achieved higher degradation rates of plant saponins such as avenacoside A (10-40 % degradation) and soyasaponin B (55-75 % degradation) present, correlated with their β-glucosidase activity (30-50 U/mL). Strict heterofermentative LABs such as Leuconostoc spp. strains were significantly better at removing hexanal, pentanal, benzaldehyde, and nonanal up to 85 % after 6 h. Finally, 384 combinations of 2 and 3 LAB selected strains (L. plantarum - L. mesenteroides - L. pseudomesenteroides) were tested at different strain-ratios, which demonstrated synergistic effects at degrading ferulic acid to more than 80 %, increasing acidification rates, and producing higher concentrations of diacetyl and acetoin (up to 3.28 and 28.13 µg/g sample) when L. pseudomesenteroides 1993 was included in the mix. This study demonstrated the potential of using unconventional plant-adapted LAB strains as starter cultures for the elimination of multiple unwanted compounds for the development of higher quality PBFDA without the use of conventional dairy-based LAB isolates. Finally, the screening approach could be used for microbial screening purposes throughout the development of starter cultures for plant-based yogurts, cheese, and other non-dairy fermented products.

In-situ substitution and community dynamics modeling for enhanced safety in Chinese rice wine brewing

This research paper focuses on the application of the "Design-Build-Test-Learn" framework to design and evaluate a synthetic microbial community aimed at studying the impact of Lactic Acid Bacteria (LAB) interactions and fitness on the formation of biogenic amines (BAs) in Chinese rice wine (CRW). The study reveals a close correlation between the assembly model of LAB and the accumulation of BAs in CRW, and multiple interactions were observed between amine-producing and non-amine-producing LAB, including commensalism, amensalism, and competition. The commensalism among amine-producing LAB was found to promote BAs accumulation through metabolic cross-feeding of amino acids. Moreover, the higher-order interaction community was designed to regulate the BAs formation effectively. For instance, the interference of Lactiplantibacillus plantarum (ACBC271) resulted in the elimination of amine-producing LAB viability, resulting in a 22% decrease (not exceeding 43.54 mg/L) in the total amount of BAs. Simulation of community dynamics models further suggests that LAB with quantitative social interactions can effectively control LAB accumulation in CRW by forecasting fluctuation in BAs generation through fitness competition and metabolic interference. Overall, this study provides valuable insights into the complex interaction networks within microbial communities in traditional fermentation ecosystems. It also proposes a novel approach for quality control of nitrogen food safety factors in fermented foods.

Highly efficient reduction of ammonia emissions from livestock waste by the synergy of novel manure acidification and inhibition of ureolytic bacteria

The global livestock system is one of the largest sources of ammonia emissions and there is an urgent need for ammonia mitigation. Here, we designed and constructed a novel strategy to abate ammonia emissions via livestock manure acidification based on a synthetic lactic acid bacteria community (LAB SynCom). The LAB SynCom possessed a wide carbon source spectrum and pH profile, high adaptability to the manure environment, and a high capability of generating lactic acid. The mitigation strategy was optimized based on the test and performance by adjusting the LAB SynCom inoculation ratio and the adding frequency of carbon source, which contributed to a total ammonia reduction efficiency of 95.5 %. Furthermore, 16S rDNA amplicon sequencing analysis revealed that the LAB SynCom treatment reshaped the manure microbial community structure. Importantly, 22 manure ureolytic microbial genera and urea hydrolysis were notably inhibited by the LAB SynCom treatment during the treatment process. These findings provide new insight into manure acidification that the conversion from ammonia to ammonium ions and the inhibition of ureolytic bacteria exerted a synergistic effect on ammonia mitigation. This work systematically developed a novel strategy to mitigate ammonia emissions from livestock waste, which is a crucial step forward from traditional manure acidification to novel and environmental-friendly acidification.

In silico prediction of potential indigenous microbial biomarkers in Penaeus vannamei identified through meta-analysis and genome-scale metabolic modelling

BACKGROUND

Understanding the microbiome is crucial as it contributes to the metabolic health of the host and, upon dysbiosis, may influence disease development. With the recent surge in high-throughput sequencing technology, the availability of microbial genomic data has increased dramatically. Amplicon sequence-based analyses majorly profile microbial abundance and determine taxonomic markers. Furthermore, the availability of genome sequences for various microbial organisms has prompted the integration of genome-scale metabolic modelling that provides insights into the metabolic interactions influencing host health. However, the analysis from a single study may not be consistent, necessitating a meta-analysis.

RESULTS

We conducted a meta-analysis and integrated with constraint-based metabolic modelling approach, focusing on the microbiome of pacific white shrimp Penaeus vannamei, an extensively cultured marine candidate species. Meta-analysis revealed that Acinetobacter and Alteromonas are significant indicators of "health" and "disease" specific taxonomic biomarkers, respectively. Further, we enumerated metabolic interactions among the taxonomic biomarkers by applying a constraint-based approach to the community metabolic models (4416 pairs). Under different nutrient environments, a constraint-based flux simulation identified five beneficial species: Acinetobacter spWCHA55, Acinetobacter tandoii SE63, Bifidobacterium pseudolongum 49 D6, Brevundimonas pondensis LVF1, and Lutibacter profundi LP1 mediating parasitic interactions majorly under sucrose environment in the pairwise community. The study also reports the healthy biomarkers that can co-exist and have functionally dependent relationships to maintain a healthy state in the host.

CONCLUSIONS

Toward this, we collected and re-analysed the amplicon sequence data of P. vannamei (encompassing 117 healthy and 142 disease datasets). By capturing the taxonomic biomarkers and modelling the metabolic interaction between them, our study provides a valuable resource, a first-of-its-kind analysis in aquaculture scenario toward a sustainable shrimp farming.

Investigation of two metabolic engineering approaches for (R,R)-2,3-butanediol production from glycerol in Bacillus subtilis

BACKGROUND

Flux Balance Analysis (FBA) is a well-known bioinformatics tool for metabolic engineering design. Previously, we have successfully used single-level FBA to design metabolic fluxes in Bacillus subtilis to enhance (R,R)-2,3-butanediol (2,3-BD) production from glycerol. OptKnock is another powerful technique for devising gene deletion strategies to maximize microbial growth coupling with improved biochemical production. It has never been used in B. subtilis. In this study, we aimed to compare the use of single-level FBA and OptKnock for designing enhanced 2,3-BD production from glycerol in B. subtilis.

RESULTS

Single-level FBA and OptKnock were used to design metabolic engineering approaches for B. subtilis to enhance 2,3-BD production from glycerol. Single-level FBA indicated that deletion of ackA, pta, lctE, and mmgA would improve the production of 2,3-BD from glycerol, while OptKnock simulation suggested the deletion of ackA, pta, mmgA, and zwf. Consequently, strains LM01 (single-level FBA-based) and MZ02 (OptKnock-based) were constructed, and their capacity to produce 2,3-BD from glycerol was investigated. The deletion of multiple genes did not negatively affect strain growth and glycerol utilization. The highest 2,3-BD production was detected in strain LM01. Strain MZ02 produced 2,3-BD at a similar level as the wild type, indicating that the OptKnock prediction was erroneous. Two-step FBA was performed to examine the reason for the erroneous OptKnock prediction. Interestingly, we newly found that zwf gene deletion in strain MZ02 improved lactate production, which has never been reported to date. The predictions of single-level FBA for strain MZ02 were in line with experimental findings.

CONCLUSIONS

We showed that single-level FBA is an effective approach for metabolic design and manipulation to enhance 2,3-BD production from glycerol in B. subtilis. Further, while this approach predicted the phenotypes of generated strains with high precision, OptKnock prediction was not accurate. We suggest that OptKnock modelling predictions be evaluated by using single-level FBA to ensure the accuracy of metabolic pathway design. Furthermore, the zwf gene knockout resulted in the change of metabolic fluxes to enhance the lactate productivity.

LACpG10-HL Functions Effectively in Antibiotic-Free and Healthy Husbandry by Improving the Innate Immunity

Antibiotics are broadly restricted in modern husbandry farming, necessitating the need for efficient and low-cost immunomodulatory preparations in antibiotic-free and healthful farming. As is known to all, CpG oligonucleotides (CpG-ODNs, an effective innate immunostimulatory agent) recognized by TLR9 in mammals (while TLR21 in avians) could collaborate with some united agent to induce stronger immune responses, but the cost is prohibitively expensive for farmers. Here, considering the coordination between TLR2 and TLR9/TLR21, we firstly proposed the idea that the well-fermented Lactococcus lactis could be utilized as a CpG-plasmid carrier (LACpG10) to enhance the host’s innate immunity against pathogenic invasion. In the present study, after obtaining LACpG10-HL from homogenized and lyophilized recombinant strain LACpG10, we treated primary chicken lymphocytes, two cell lines (HD11 and IPEC-J2), and chickens with LACpG10-HL, CpG plasmids (pNZ8148-CpG10), and other stimulants, and respectively confirmed the effects by conducting qRT-PCR, bacterial infection assays, and a zoological experiment. Our data showed that LACpG10-HL could induce excellent innate immunity by regulating autophagy reactions, cytokine expression, and motivating PRRs. Interestingly, despite having no direct antiseptic effect, LACpG10-HL improved the antibacterial capacities of lymphocytes and enterocytes at the first line of defense. Most importantly, water-supplied LACpG10-HL treatment reduced the average adverse event rates, demonstrating that LACpG10-HL maintained its excellent immunostimulatory and protective properties under farming conditions. Our research not only contributes to revealing the satisfactory effects of LACpG10-HL but also sheds new light on a cost-effective solution with optimal immune effects in green, antibiotic-free, and healthful husbandry farming.