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The networks of the gut microbiome facilitate cross-feeding between microbial components that have direct effects on the host. Changes in the abundance of microorganisms or metabolites contribute to the pathogenesis of recurrent Clostridioides difficile infection, inflammatory bowel diseases, metabolic diseases, and cancer. Fecal microbiota transplantation (FMT) is an emerging experimental therapy with potential to treat various microbiome-associated disorders, although the mechanisms underlying its potential success remain unknown. Current theories propose that FMT success lies in the ability of its transferred microbes to resist pathogen colonization or exert immunomodulatory effects on the host. Unraveling the effects of fecal components and trans-kingdom interactions in the efficacy of FMT therapies will allow for personalized treatment of microbiome-associated diseases. Fecal microbiota transplantation (FMT) has emerged as an alternative or adjunct experimental therapy for microbiome-associated diseases following its success in the treatment of recurrent Clostridioides difficile infections (rCDIs). However, the mechanisms of action involved remain relatively unknown. The term 'dysbiosis' has been used to describe microbial imbalances in relation to disease, but this traditional definition fails to consider the complex cross-feeding networks that define the stability of the microbiome. Emerging research transitions toward the targeted restoration of microbial functional networks in treating different diseases. In this review, we explore potential mechanisms responsible for the efficacy of FMT and future therapeutic applications, while revisiting definitions of 'dysbiosis' in favor of functional network restoration in rCDI, inflammatory bowel diseases (IBDs), metabolic diseases, and cancer. [ABSTRACT FROM AUTHOR]

[Display omitted] • Using acetate is not advantageous for improving performance of manure-fed MECs. • Cross-feeding lowers methane production performance during electromethanogenesis. • To produce similar CH 4 from manure as acetate, two times greater sCOD is required. • Model exoelectrogen Geobacter dominated the anodes of all manure-fed MECs. • Hydrogenotrophic Methanoculleus is abundant on the cathodes of manure-fed MECs. This study qualitatively assessed the impacts of different start-up strategies on the performance of methane (CH 4) production from cattle manure (CM) in electromethanogenic reactors. Single chamber MECs were operated with an applied voltage of 0.7 V and the impact of electrode acclimatization with a simple substrate, acetate (ACE) vs a complex waste, CM, was compared. Upon biofilm formation on the sole carbon source (ACE or CM), several MECs (ACE_CM and CM_ACE) were subjected to cross-feeding (switching substrate to CM or ACE) during the test period to evaluate the impact of the primary substrate. Even though there was twice as much peak current density via feeding ACE during biofilm formation, this did not translate into higher CH 4 production during the test period, when reactors were fed with CM. Higher or similar CH 4 production was recorded in CM_CM reactors compared to ACE_CM at various soluble chemical oxygen demand (sCOD) concentrations. Additionally, feeding ACE as primary substrate did not significantly impact either COD removals or coulombic efficiencies. On the other hand, the use of anaerobic digester (AD) seed as an inoculum in CM-fed MECs (CM_CM), relative to no inoculum added MECs (Blank), increased the initial CH 4 production rate by 45% and reduced the start-up time by 20%. In CM-fed MECs, Geobacter dominated bacterial communities of bioanodes and hydrogenotrophic methanogen Methanoculleus dominated archaeal communities of biocathodes. Community cluster analysis revealed the significance of primary substrate in shaping electrode biofilm; thus, it should be carefully selected for successful start-up of electromethanogenic reactors treating wastes. [ABSTRACT FROM AUTHOR]

The recalcitrance and physiochemical complexity of lignocellulosic biomass limit its hydrolysis and subsequent anaerobic digestion to produce biomethane. Restricted lignocellulose hydrolysis reduces the substrate supply to catabolic pathways of anaerobic digestion, altering the indigenous digester microbiota by affecting the syntrophy between hydrolytic, acidogenic, and acetogenic bacterial and methanogenic archaeal communities. This can considerably impede the maximum utilization of this potential biomass resource, resulting in poor biomass-to-biomethane conversion. Bioaugmentation of anaerobic digestion with potent lignocellulolytic microbes can enhance rate-limiting hydrolytic pathways to convert lignocellulosic biomass into biomethane efficiently. Bioaugmentation can enrich lignocellulose-degrading microbiota in digesters through complementary metabolic and transcription processes. Although the positive roles of bioaugmentation in improving lignocellulose digestion have been well-established, efforts are still underway to properly attribute the role of bioaugmentation to specific microbiota compositions and their metabolic functions. Assessing the stability, dynamics, and specific metabolic roles of different microbial guilds of the bioaugmenting lignocellulolytic microbiota and their intricate interactions with the indigenous microbiota, along with deterministic process factors, is pivotal for the successful real-scale execution of bioaugmented lignocellulose digestion. To clarify, studies have adopted an integrated approach of high-throughput meta-omics to identify the unique metabolic functional niches filled by core microbial communities in bioaugmented digester microbiota. Enhanced bioconversion of lignocellulosic biomass into methane can considerably contribute to the Sustainable Development Goals by addressing affordable and clean energy production. This review emphasizes the significance of lignocellulolytic microbiotas in bioaugmentation of anaerobic digestion and the understanding of their ecological functions in the intricate interspecies nexus during biomethanation. [Display omitted] • Low digestibility of lignocellulosic biomass hampers its anaerobic digestion (AD). • Bioaugmentation (BA) boosts lignocellulose degradation and substrate availability. • BA efficacy depends on stability and functional resilience of microbiota in AD. • Real-scale BA in AD requires understanding microbial dynamics and interactions. [ABSTRACT FROM AUTHOR]

• GEMs were developed for the static and QS-based dynamic regulation strategies. • Productivity and stability of two-strain cocultivations were systematically investigated. • How QS crosstalk affect the dynamics of the co-culture system was evaluated. • Performances and characteristics of the three different QSCNs were compared. Quorum sensing (QS), a dynamic microbial communication mechanism, has been widely applied to synthetic biology for different functions. The incorporation of genome-scale models (GEMs) provides a powerful tool for understanding the metabolic capabilities and interactions within microbial communities. However, the introduction of the relevant QS devices for the stability and productivity of the microbial community lacks systematic analysis, let alone the GEMs-based rational design and optimization of QS-regulated microbial ecosystems. In this study, we integrated different QS regulation strategies with the metabolic division of labor to establish a combinational GEM for systematically designing and optimizing the process of the two-strain cross-feeding cocultivation. Specifically, taking the production of salidroside within two cross-feeding fermentation as an example, the GEMs were developed for the static and QS-based dynamic regulation strategies, and the corresponding simulation and optimization were performed. Then, we further constructed the QS-based self-regulating, cross-regulating, and hybrid-regulating QS communication network (QSCN) by using synthetic biology toolkits to investigate the productivity and stability of cross-feeding cocultivation. Results showed that the hybrid QSCN can better realize the cell density control and the improvement of productivity (562.57 mg/L). This study offers insights for developing more comprehensive model and regulation strategies for QS-based control in diverse applications. [ABSTRACT FROM AUTHOR]

Microplastics (MPs) are frequently detected in the wastewater. Herein, the short-term and long-term effects of polyethylene terephthalate (PET) MPs on anammox granular sludge were investigated and the potential response mechanisms were analyzed. Results showed that although short-term exposure of anammox granular sludge to PET-MPs induced a stress response, the nitrogen removal performance was not significantly affected. By contrast, long-term exposure to PET-MPs inhibited nitrogen removal performance with increased exposure time and PET-MP concentration. The total nitrogen removal efficiency (TNRE) decreased by 28.7 % when sludge was exposed to 200 mg/L of PET-MPs. However, the anammox activity recovered with prolonged operation time, and approximately 87 % of the initial TNRE was recovered after three months. Microbial community evolution and metabolic exchange variations were the potential response mechanisms of anammox granular sludge to PET-MP exposure, with PET-MP exposure decreasing the anammox bacteria growth rate and relative symbiotic bacterial abundance in the anammox consortia and hindering cross-feeding pathways. The findings of this study provide novel insight into anammox behavior when treating wastewater containing PET-MPs. [Display omitted] • Short- and long-term responses of anammox granular sludge to PET-MPs are evaluated. • Nitrogen removal was inhibited with increased MPs exposure time and concentration. • Anammox activity was effectively recovered after long-term acclimatization. • PET-MP exposure decreased the AnAOB growth rate and symbiotic bacteria abundance. • Microbial evolution and metabolic exchange variations were response mechanisms [ABSTRACT FROM AUTHOR]

[Display omitted] • Applied voltage promoted the formation of primary electrode biofilms. • Applied voltage increased biomass of electrode biofilms by approximately 70 % or 100 %. • Starting up MEC-AD at 0.8 V using WAS without seeding AD sludge was feasible. • Part of the core functional microorganisms were enriched during start-up period. Applied voltage is a crucial parameter in hybrid microbial electrolysis cells-anaerobic digestion (MEC-AD) systems for enhancing methane production from waste activated sludge (WAS). This study explored the impact of applied voltage on the initial biofilm formation on electrodes during the MEC-AD startup using raw WAS (Rr) and heat-pretreated WAS (Rh). The findings indicated that the maximum methane productivity for Rr and Rh were 3.4 ± 0.5 and 3.4 ± 0.2 mL/gVSS/d, respectively, increasing 1.5 times and 2.6 times over the productivity at 0 V. The biomass on electrode biofilms for Rr and Rh at 0.8 V increased by 70 % and 100 % compared to 0 V. The core functional microorganisms in the cathode biofilm were Methanobacterium and Syntrophomonas , and Geobacter in the anode biofilm, enhancing methane production through syntrophism and direct interspecies electron transfer, respectively. These results offer academic insights into optimizing AD functional electrode biofilms by applying voltage. [ABSTRACT FROM AUTHOR]

Natural polysaccharides have complex structural properties and a wide range of health-promoting effects. Accumulating evidence suggests that the effects are significantly mediated through fermentation by gut microbiota. In recent years, the relationship between the structures of natural polysaccharides and their properties in regulating gut microbiota has garnered significant research attention as researchers attempt to precisely understand the role of gut microbiota in the bioactivities of natural polysaccharides. Progress in this niche, however, remains limited. In this review, we first provide an overview of current research investigating this structure-property relationship. We then present a detailed correlation analysis between the structural characteristics of 159 purified natural polysaccharides and their effects on gut microbiota reported over the past two decades. The analysis revealed that diverse gut bacteria show specific correlations with the molecular weight, glycosidic linkages, and monosaccharide composition of natural polysaccharides. Multifaceted molecular mechanisms, including carbohydrate binding, enzymatic degradation, and cross-feeding, were proposed to be collectively involved in these correlations. Finally, we offer our perspective on future studies to further improve our understanding of the relationship between polysaccharide structure and gut microbiota regulation. [Display omitted] [ABSTRACT FROM AUTHOR]

Dietary polysaccharides function not only as indispensable nutrients and energy sources for the host organism but also as critical substrates for the gut microbiota. Gut microorganisms possess the ability to selectively degrade and metabolize specific dietary polysaccharides, thus fostering their proliferation and yielding crucial bioactive metabolites that potentially influence host metabolic and immune pathways. Dysbiosis of the gut microbiota has been extensively documented to be closely linked with the onset and progression of various diseases; in this regard, the precision modulation strategy of the gut microbiome via dietary polysaccharides holds substantial potential to enhance human health. Here, we delve into the therapeutic potential of dietary polysaccharides for the precision modulation of specific gut microorganisms via dietary interventions, with particular emphasis on their implications for the prevention and management of metabolic and inflammatory disorders. Given the complexity of the human gut microbiome and the varying degrees to which different bacterial members utilize carbohydrates, we conduct an in-depth analysis of the differential utilization of dietary polysaccharides by key gut microbiome, with particular emphasis on the role of carbohydrate-active enzymes in these processes. Furthermore, we elucidate the pivotal role of carbohydrate utilization within microbial cross-feeding networks and its significance in maintaining gut homeostasis. In summary, this review investigates the precision modulation of gut microbiota through dietary polysaccharides, with the aim of establishing a theoretical foundation for the development of personalized nutritional interventions. These strategies hold substantial potential for enhancing human health and offer valuable opportunities for the prevention and treatment of microbiota-associated diseases. • CAZymes drive species-specific polysaccharide utilization in gut bacteria. • Polysaccharide-based microbiota precise modulation shows health-promoting potential. • Microbial cross-feeding networks are key to maintaining gut microbiome balance. • Tailored dietary interventions present promising strategies for disease prevention. [ABSTRACT FROM AUTHOR]

[Display omitted] • The coupled system achieved a maximum nitrogen removal efficiency of 97.8%. • Decreasing thiosulfate and raising nitrogen load boosted functional species growth. • Microbial cross-feeding and self-adaptation strategies were key mechanisms. A coupled thiosulfate-driven denitrification and anammox (TDDA) process was established to remove nitrogen from wastewater. It was optimized in an up-flow anaerobic sludge blanket reactor using synthetic wastewater, and its reliability was then verified with actual wastewater. The results demonstrated that nitrate, nitrite, and ammonium could be synergistically removed, and the highest total nitrogen removal efficiency reached 97.8% at a loading of 1.39 kgN/(m3·d). Anammox bacteria, primarily Candidatus_Brocadia , were the main contributors to nitrogen removal, while sulfur-oxidizing bacteria such as Thiobacillus and Rhodanobacter played a supportive role. By optimizing substrate conditions to enhance the anammox process, the coupled system attained higher abundances of functional genes such as napA , nirS , hzs , soxXA , and soxYZ , along with the corresponding microbial species. The data suggested that microbial cross-feeding and self-adaptation strategies were key to efficient nitrogen removal by TDDA. [ABSTRACT FROM AUTHOR]

• Granule-based anammox reactor achieves a stable and high NLR with folate dosage. • Folate dosage leads to the granular floatation potential decreasing by 67.1%. • EPS decline and surface pore plugging dredge contribute to floatation control. • Anammox bacteria reduce EPS secretion due to attenuated cross-feeding after adding folate. Although granular floatation has been recognized as a significant issue hindering the application of high-rate anammox biotechnology, limited knowledge is available about its causes and control strategies. This study proposed a novel control strategy by adding folate, and demonstrated its role in the granular floatation alleviation through long-term operation and granular characterizations. It was found that the floatation of anammox granular sludge was obviously relieved with the decreased sludge floatation potential by 67.1% after dosing with folate (8 mg/L) at a high nitrogen loading rate of 12.3 kg-N/(m3·d). Physiochemical analyses showed that the decrease of extracellular polymeric substances (EPS) content (mainly protein), the alleviation of granular surface pore plugging in conjunction with the smooth discharge of generated nitrogen gas were collectively responsible for efficient floatation control. Moreover, metagenomic analysis suggested that the synergistic interactions between anammox bacteria and their symbionts were attenuated after dosing exogenous folate. Anammox bacteria would reduce their synergistic dependence on the symbionts, and decline the supply of metabolites (e.g., amino acids and carbohydrates in EPS) to symbiotic bacteria. The declined EPS excretion contributed to the alleviation of granular floatation by dredging pores blockage, thus leading to a stable system performance. The findings not only offer insights into the role of microbial interaction in granular sludge floatation, but also provide a feasible approach for controlling the floatation issue in anammox granular-based processes. [Display omitted] [ABSTRACT FROM AUTHOR]

Constructing a traceable synthetic community represents an efficacious strategy for enhancing the quality and standardization of traditional spontaneous food fermentations. In this study, we engineered a community comprising one precursor metabolic strain (Module I: capable of converting ferulic acid to 4-vinyl guaiacol) and seven product-forming strains (Module II: facilitating the conversion of 4-vinyl guaiacol to 4-ethyl guaiacol) to optimize guaiacols metabolism. Notably, the tri-culture consortium exhibited superior efficiency compared to pent-culture, quad-culture, bi-cultures, and mono-culture configurations, particularly when comprised of a Wickerhamomyces anomalus strain (Module I) and two bacterial strains (Module II: Pantoea sp. and Bacillus altitudinis). This tri-culture system demonstrated collaborative carbon source cross-feeding to produce 4-ethyl guaiacol between Module I and Module II, with synergistic interactions observed between the two bacterial strains in the conversion of 4-vinyl guaiacol to 4-ethyl guaiacol within Module II. Additionally, the competitive dynamics were observed among members of Module II in the conversion of 4-vinyl guaiacol to 4-ethyl guaiacol, with the number of Module II strains increasing from three to seven. Thus, we established a specialized community for modulating guaiacol metabolism, offering insights for the development of healthier products and advancement in modern food fermentations. [ABSTRACT FROM AUTHOR]

Microbial metabolism in landfill leachate systems is critically important in driving the degradation reactions of organic pollutants, including the emerging pollutant bisphenol A (BPA). However, little research has addressed the microbial degradation of BPA in landfill leachate and its interactions with nitrogen (N), sulfur (S), and methane (CH 4) metabolism on a global scale. To this end, in this study on a global scale, an extremely high concentration of BPA was detected throughout the global landfill leachates. Subsequent reconstructive analyses of metagenomic datasets from 113 sites worldwide revealed that the predominant BPA-degrading microflora included Proteobacteria, Firmicutes, and Bacteroidota. Further metabolic analyses revealed that all four biochemical pathways involved in the degradation of BPA were achieved through biochemical cooperation between different bacterial members of the community. In addition, BPA degraders have also been found to actively collaborate synergistically with non-BPA degraders in the N and S removal as well as CH 4 catabolism in landfill leachates. Collectively, this study not only provides insights into the dominant microbial communities and specific types of BPA-degrading microbial members in the community of landfill leachates worldwide, but also reveals the synergistic interactions between BPA mineralization and N, S, and CH 4 metabolism. These findings offer valuable and important insights for future comprehensive and in-depth investigations into BPA metabolism in different environments. [Display omitted] • High BPA concentration was detected throughout the global 114 landfill site leachates. • Proteobacteria , Firmicutes , and Bacteroidota were the predominant microbes in the microbiomes. • BPA-degraders were primarily distributed in Proteobacteria , Firmicutes , and Bacteroidota. • No single strain or MAG was capable of the complete degradation or mineralization of BPA. • Synergistic interactions were evident between BPA mineralization and N, S, and CH 4 metabolism. [ABSTRACT FROM AUTHOR]

• TNRE increased to 87.89 ± 1.82 % after dosing low concentration exogenous glycine. • Candidatus Brocadia and Candidatus Kuenenia emerged as primary enriched genus. • Glycine modulated nitrogen metabolism by altering the content of Hzs & NirS genes. • High dose of exogenous gly in cross-feeding broke the equilibrium of anammox system. • Gly cleavage system could be the initiating point for the cross-feeding imbalance. Strategies to break the cross-feeding equilibrium by dosing essential metabolites and thus enriching and isolating anammox bacteria (AnAOB) have been proposed, but amino acids have not been investigated as important cross-feeding pathways in anammox consortia. In this study, long-term experiments were designed to verify the effect of exgenous glycine on anammox consortia and changes in the bacterial community and metabolic activity after the addition of glycine in a highly active anammox system were investigated. The results showed that the impact of glycine on the activity of anammox highly depended on glycine concentrations, which was manifested as a promotive effect at low concentrations (0–150 mg/L) and an inhibitory effect at high concentrations (300–600 mg/L). The addition of low concentrations of glycine not only enhanced the diversity and richness of bacterial communities but also promoted the enrichment of Candidatus Kuenenia. The qPCR results showed that the content of functional genes Hzs, NirS and anammox 16S rRNA increased while the expression of amoA and NrfA genes was suppressed when glycine acted positively on AnAOB; Hzs and amoA were suppressed when glycine acted negatively on AnAOB, while the expression of NirS and NrfA genes increased dramatically. Specific anammox activity (SAA) experimental results show that 50–150 mg/L glycine was the optimal amount for promoting the activity of AnAOB. Analysis of community metabolic functions indicated that the addition of exogenous glycine resulted in a imbalance of glycine cross-feeding and promoted AnAOB enrichment mainly by affecting pathways such as other glycan degradation and Lysosome. Overall, this study provided new insights into understanding the glycine cross-feeding, which is essential for improving anammox-based technologies. [ABSTRACT FROM AUTHOR]

Metabolic cross-feeding is a pervasive interaction between bacteria to acquire novel phenotypes. However, our current understanding of the survival mechanism for cross-feeding in cocultured bacterial biofilms under heavy-metal conditions remains limited. Herein, we found that Comamonas sp. A23 produces L-phenylalanine to activate the L-phenylalanine degradation pathway in Enterobacter sp. A11, enhancing biofilm formation and cadmium [Cd(II)] immobilization in A11. The genes responsible for L-phenylalanine-degradation (paaK) and cell attachment and aggregation (csgAD) are essential for biofilm formation and Cd(II) immobilization in A11 induced by L-phenylalanine. The augmentation of A11 biofilms, in turn, protects A23 under Cd(II) and H 2 O 2 stresses. The plant-based experiments demonstrate that the induction of two rice Cd(II) transporters, OsCOPT4 and OsBCP1 , by A11 and A23 enhances rice resistance against Cd(II) and H 2 O 2 stresses. Overall, our findings unveil the mutual dependence between bacteria and rice on L-phenylalanine cross-feeding for survival under abiotic stress. [ABSTRACT FROM AUTHOR]

• Enhanced anaerobic toluene degradation synchronously promotes methane production. • Electro-stimulation alters syntrophic interactions within anaerobic microbiota. • f_Syntrophobacteraceae MAG116 was identified as a syntrophic toluene degrader. • Electroselection favored Methanobacterium -dominated hydrogenotrophic methanogenesis. • Desulfoprunum sp. proposed as a novel electrogen involved in electron syntrophy. Syntrophy achieved via microbial cooperation is vital for anaerobic hydrocarbon degradation and methanogenesis. However, limited understanding of the metabolic division of labor and electronic interactions in electro-stimulated microbiota has impeded the development of enhanced biotechnologies for degrading hydrocarbons to methane. Here, compared to the non-electro-stimulated methanogenic toluene-degrading microbiota, electro-stimulation at 800 mV promoted toluene degradation and methane production efficiencies by 11.49 %-14.76 % and 75.58 %-290.11 %, respectively. Hydrocarbon-degrading gene bamA amplification and metagenomic sequencing analyses revealed that f_Syntrophobacteraceae MAG116 may act as a toluene degrader in the non-electro-stimulated microbiota, which was proposed to establish electron syntrophy with the acetoclastic methanogen Methanosarcina spp. (or Methanothrix sp.) through e-pili or shared acetate. In the electro-stimulated microbiota, 37.22 ± 4.33 % of Desulfoprunum sp. (affiliated f_Desulfurivibrionaceae MAG10) and 58.82 ± 3.74 % of the hydrogenotrophic methanogen Methanobacterium sp. MAG74 were specifically recruited to the anode and cathode, respectively. The potential electrogen f_Desulfurivibrionaceae MAG10 engaged in interspecies electron transfer with both syntroph f_Syntrophobacteraceae MAG116 and the anode, which might be facilitated by c- type cytochromes (e.g., ImcH, OmcT, and PilZ). Moreover, upon capturing electrons from the external circuit, the hydrogen-producing electrotroph Aminidesulfovibrio sp. MAG60 could share electrons and hydrogen with the methanogen Methanobacterium sp. MAG74, which uniquely harbored hydrogenase genes ehaA-R and ehbA-P. This study elucidates the microbial interaction mechanisms underlying the enhanced metabolic efficiency of the electro-stimulated methanogenic toluene-degrading microbiota, and emphasizes the significance of metabolic and electron syntrophic interactions in maintaining the stability of microbial community functionality. [Display omitted] [ABSTRACT FROM AUTHOR]

Resistant starch (RS) can potentially prevent type 2 diabetes through the modulation of intestinal microbiota and microbial metabolites. Currently, it has been wildly noted that altering the intestinal microbial composition and short-chain fatty acids levels can achieve therapeutic effects, although the specific mechanisms were rarely elucidated. This review systematically explores the structural characteristics of different RS, analyzes the cross-feeding mechanism utilized by intestinal microbiota, and outlines the pathways and targets of butyrate, a primary microbial metabolite, for treating diabetes. Different RS types may have a unique impact on microbiota composition and their cross-feeding, thus exploring regulatory mechanisms of RS on diabetes through intestinal flora interaction and their metabolites could pave the way for more effective treatment outcomes for host health. Furthermore, by understanding the mechanisms of strain-level cross-feeding and metabolites of RS, precise dietary supplementation methods targeted at intestinal composition and metabolites can be achieved to improve T2DM. [ABSTRACT FROM AUTHOR]

Lignin, a major component of plant biomass, remains underutilized for renewable biofuels due to its complex and heterogeneous structure. Although investigations into depolymerizing lignin using fungi are well-established, studies of microbial pathways that enable anaerobic lignin breakdown linked with methanogenesis are limited. Through an enrichment cultivation approach with inoculation of freshwater sediment, we enriched a microbial community capable of producing methane during anaerobic lignin degradation. We reconstructed the near-complete population genomes of key lignin degraders and methanogens using metagenome-assembled genomes finally selected in this study (MAGs; 92 bacterial and 4 archaeal MAGs affiliated into 45 and 2 taxonomic groups, respectively). This study provides genetic evidence of microbial interdependence in conversion of lignin to methane in a syntrophic community. Metagenomic analysis revealed metabolic linkages, with lignin-hydrolyzing and/or fermentative bacteria such as the genera Alkalibaculum and Propionispora transforming lignin breakdown products into compounds such as acetate to feed methanogens (two archaeal MAGs classified into the genus Methanosarcina or UBA6 of the family Methanomassiliicoccaceae). Understanding the synergistic relationships between microbes that convert lignin could inform strategies for producing renewable bioenergy and treating aromatic-contaminated environments through anaerobic biodegradation processes. Overall, this study offers fundamental insights into complex community-level anaerobic lignin metabolism, highlighting hitherto unknown players, interactions, and pathways in this biotechnologically valuable process. [Display omitted] • Metagenomic analysis revealed metabolic linkages between lignin-degrading bacteria and methanogens. • Bacteria transform lignin breakdown products into compounds like acetate to feed methanogens. • Methanogen studied showed potential for utilization of lignin-derived materials and capable of vitamin B 12 biosynthesis in UBA6 group. • Unraveling synergistic interactions facilitates biotechnological applications in bioenergy and environmental remediation. [ABSTRACT FROM AUTHOR]

Fucose-containing oligosaccharides exhibit various biological activities, particularly for improving the intestinal health of infants. Bacterial exopolysaccharides are promising resource of fucose-containing oligosaccharides. A fucose-containing trisaccharide (d - Glc p-β-(1 → 4)- l - Fuc p and d - Gal p-α-(1 → 3)- l - Fuc p, GuFGa) with same monosaccharide composition with 2′-fucosyllactose (2′-FL, the most abundant oligosaccharide in human milk), is obtained from bacterial exopolysaccharides. This study compared the in vitro prebiotic activities of GuFGa and 2′-FL using mono- and co-culture fermentation. Mono-culture shows GuFGa could be utilized by Bifidobacterium infantis and Lactobacillus plantarum , while 2′-FL only promote the proliferation of B. infantis. Co-culture fermentation involves cross-feeding between B. infantis and L. plantarum to utilize GuFGa. Further in vitro fecal microbiota fermentation of breastfed infants demonstrates that GuFGa exhibits better prebiotic activity than 2′-FL in increasing beneficial bacteria (Bifidobacterium and Lactobacillus) abundance and reducing harmful bacteria (Clostridium _ sensu _ stricto and Escherichia - Shigella) abundance. Moreover, GuFGa and 2′-FL fermentation shifted the gut microbiota composition of formula-fed infants to that of breastfed infants. Furthermore, herein, GuFGa and 2′-FL caused distinct metabolic profiles in both short-chain fatty acids and indole derivatives (e.g. indolelactic acid and indolepropionic acid). In summary, this study provides insights into the exploration of novel functional fucose-containing oligosaccharides as potential prebiotics. [Display omitted] • Cross-feeding were observed in utilizing bacterial GuFGa. • Effect of GuFGa or 2′-fucosyllactose fermentation on breastfed or formula-fed infant fecal microbiota was evaluated. • GuFGa exhibited better in vitro prebiotic activity than 2′-fucosyllactose. • GuFGa promoted the production of indolelactic acid and indolepropionic acid. [ABSTRACT FROM AUTHOR]

• Establishment of host–microbe interactions has facilitated co-evolution between the host and its resident intestinal microbiota. • These mutualistic relationships are particularly important for developmental processes of the host during early life. • Members of the infant gut microbiota establish microbe-microbe interactions such as syntrophy or cross-feeding behavior. • Bifidobacteria are key members of the infant gut microbiota that possess adaptative traits suited to the intestinal ecological niche. • Host-microorganism interactions are mediated by a variety of molecular mechanisms that benefit both. Current scientific literature has identified the infant gut microbiota as a multifaceted organ influencing a range of aspects of host-health and development. Many scientific studies have focused on characterizing the main microbial taxa that constitute the resident bacterial population of the infant gut. This has generated a wealth of information on the bacterial composition of the infant gut microbiota, and on the functional role/s exerted by their key microbial members. In this context, one of the most prevalent, abundant and investigated microbial taxon in the human infant gut is the genus Bifidobacterium , due to the purported beneficial activities is bestows upon its host. This review discusses the most recent findings regarding the infant gut microbiota with a particular focus on the molecular mechanisms by which bifidobacteria impact on host health and well-being. [ABSTRACT FROM AUTHOR]

• Microbial interactions are increasingly being studied in community contexts. • Common mechanisms of interaction are found across microbiomes. • Combining multiple techniques is enabling new insight into interaction mechanisms. Microbial interactions are key aspects of the biology of microbiomes. Recently, there has been a shift in the field towards studying interactions in more representative contexts, whether using multispecies model microbial communities or by looking at interactions in situ. Across diverse microbial systems, these studies have begun to identify common interaction mechanisms. These mechanisms include interactions related to toxic molecules, nutrient competition and cross-feeding, access to metals, signaling pathways, pH changes, and interactions within biofilms. Leveraging technological innovations, many of these studies have used an interdisciplinary approach combining genetic, metabolomic, imaging, and/or microfluidic techniques to gain insight into mechanisms of microbial interactions and into the impact of these interactions on microbiomes. [ABSTRACT FROM AUTHOR]

Gut microorganisms can modulate response to cancer therapies. In this issue of Cancer Cell , Teng et al. trace the gut bacteria and metabolites in rectal cancer patients over the course of neoadjuvant chemoradiotherapy and identify Bacteroides vulgatus as a driver bacterium of therapeutic resistance by supplying tumors with nucleotides. [ABSTRACT FROM AUTHOR]

• Immobilized Z. mobilis converted sucrose to ethanol that was consumed by C. cohnii. • Levansucrase (sacB) and ndh -negative double mutant Zm6- ndh-sacB was constructed. • Immobilized Zm6- ndh-sacB converted sucrose to ethanol aerobically with a high yield. • Fed-batch with Zm6- ndh-sacB fermentation medium and cocultivations were carried out. • Syntrophy with immobilized Zm6- ndh-sacB yielded C. cohnii biomass with up to 3% DHA. Marine heterotrophic dinoflagellate Crypthecodinium cohnii is an aerobic oleaginous microorganism that accumulates intracellular lipid with high content of 4,7,10,13,16,19-docosahexaenoic acid (DHA), a polyunsaturated ω−3 (22:6) fatty acid with multiple health benefits. C. cohnii can grow on glucose and ethanol, but not on sucrose or fructose. For conversion of sucrose-containing renewables to C. cohnii DHA, we investigated a syntrophic process, involving immobilized cells of ethanologenic bacterium Zymomonas mobilis for fermenting sucrose to ethanol. The non-respiring, NADH dehydrogenase-deficient Z. mobilis strain Zm6- ndh , with high ethanol yield both under anaerobic and aerobic conditions, was taken as the genetic background for inactivation of levansucrase (sacB). SacB mutation eliminated the levan-forming activity on sucrose. The double mutant Zm6- ndh - sacB cells were immobilized in Ca alginate, and applied for syntrophic conversion of sucrose to DHA of C. cohnii , either taking the ethanol-containing fermentation medium from the immobilized Z. mobilis for feeding to the C. cohnii fed-batch culture, or directly coculturing the immobilized Zm6- ndh - sacB with C. cohnii on sucrose. Both modes of cultivation produced C. cohnii CCMP 316 biomass with DHA content around 2–3 % of cell dry weight, corresponding to previously reported results for this strain on glucose. [ABSTRACT FROM AUTHOR]

[Display omitted] • Metagenomic data and GSMMs were used to analyze the association of microbiome and metabolites. • Thirty-eight high-quality MAGs (completeness >80 % and contamination <10 %) were extracted and analyzed. • Metabolic potentials for individual and community cooperation were predicted by GSMMs of high-quality MAGs. • Twelve sub-community of 23 targets were screened by cross-feeding of 38 GSMMs. The microorganisms of the pit mud (PM) of Nongxiangxing baijiu (NXXB) have an important role in the synthesis of flavor substances, and they determine attributes and quality of baijiu. Herein, we utilize metagenomics and genome-scale metabolic models (GSMMs) to investigate the microbial composition, metabolic functions in PM microbiota, as well as to identify microorganisms and communities linked to flavor compounds. Metagenomic data revealed that the most prevalent assembly of bacteria and archaea was Proteiniphilum , Caproicibacterium , Petrimonas , Lactobacillus , Clostridium , Aminobacterium , Syntrophomonas , Methanobacterium , Methanoculleus , and Methanosarcina. The important enzymes of PM were in both GH and GT family metabolism. A total of 38 high-quality metagenome-assembled genomes (MAGs) were obtained, including those at the family level (n = 13), genus level (n = 17), and species level (n = 8). GSMMs of the 38 MAGs were then constructed. From the GSMMs, individual and community capabilities respectively were predicted to be able to produce 111 metabolites and 598 metabolites. Twenty-three predicted metabolites were consistent with the metabonomics detected flavors and served as targets. Twelve sub-community of were screened by cross-feeding of 38 GSMMs. Of them, Methanobacterium , Sphaerochaeta , Muricomes intestini , Methanobacteriaceae , Synergistaceae , and Caloramator were core microorganisms for targets in each sub-community. Overall, this study of metagenomic and target-community screening could help our understanding of the metabolite–microbiome association and further bioregulation of baijiu. [ABSTRACT FROM AUTHOR]

The full exploitation of mass and energy cross-feeding relationships among subsystems of chemical industries has great potential to enhance mass-energy efficiency. This paper proposes the concept of mass-energy cross-feeding system (MECS) with pathways for mass-energy efficiency promotion. Then a mixed integer non-linear programming (MINLP) model considering quantitative regulation is formulated. Afterwards, an MECS including propane dehydrogenation, ethane cracking, synthetic urea, and synthetic HIPP and LDPE is designed to perform demonstration. Through process simulation, integration and optimization, the results show that MECS with subsystem scale factors of 53.6, 100.0, 74.6, 57.3, and 93.1 show the optimal performance in terms of atomic utilization, energy recovery, profitability, raw material cost, and carbon emission per unit of output, with results of 0.56, 0.54, 0.44, 0.696 MM$/unit, and 0.24 t/(h·unit). This work demonstrated that implementing quantitative regulation among subsystems based on cross-feeding can greatly improve comprehensive performance of chemical manufacture systems. [Display omitted] • Mass-energy cross-feeding is set as the foundamental to enhance process integration. • An efficient mass-energy cross-feeding system (MECS) is developed. • A MINLP model through quantitative regulation is formulated as optimization solution. • Case study demonstration for the ascendency of MECS on comprehensive performance. [ABSTRACT FROM AUTHOR]

Microbial interactions, particularly metabolic cross-feeding, play important roles in removing recalcitrant environmental pollutants; however, the underlying mechanisms involved in this process remain unclear. Thus, this study aimed to elucidate the mechanism by which metabolic cross-feeding occurs during synergistic dibenzofuran degradation between a highly efficient degrader, Rhodococcus sp. strain p52, and a partner incapable of utilizing dibenzofuran. A bottom-up approach combined with pairwise coculturing was used to examine metabolic cross-feeding between strain p52 and Arthrobacter sp. W06 or Achromobacter sp. D10. Pairwise coculture not only promoted bacterial pair growth but also facilitated dibenzofuran degradation. Specifically, strain p52, acting as a donor, released dibenzofuran metabolic intermediates, including salicylic acid and gentisic acid, for utilization and growth, respectively, by the partner strains W06 and D10. Both salicylic acid and gentisic acid exhibited biotoxicity, and their accumulation inhibited dibenzofuran degradation. The transcriptional activity of the genes responsible for the catabolism of dibenzofuran and its metabolic intermediates was coordinately regulated in strain p52 and its cocultivated partners, thus achieving synergistic dibenzofuran degradation. This study provides insights into microbial metabolic cross-feeding during recalcitrant environmental pollutant removal. [Display omitted] • Coculture promoted bacterial growth and enhanced dibenzofuran degradation. • Strain p52 released metabolic intermediates during dibenzofuran degradation. • The cocultivated partners could utilize dibenzofuran metabolic intermediates for growth. • The accumulation of salicylic acid and gentisic acid inhibited dibenzofuran degradation. • Catabolic gene expression was concertedly regulated in coculturing bacteria. [ABSTRACT FROM AUTHOR]

Enterococcus faecalis and Staphylococcus aureus are frequently co-isolated from biofilm-associated infections. A new study by Ch'ng et al. revealed that S. aureus -released heme feeds E. faecalis respiration, augmenting E. faecalis growth and overall biofilm biomass. Their finding further supports the theory that metabolite cross-feeding is a critical aspect shaping polymicrobial biofilm interactions. [ABSTRACT FROM AUTHOR]

• Acetate and propionate upgrading shaped similar microbial community structure. • Acetate and propionate had distinct connections with bacteria and methanogens. • SAOB and SPOB connected closely with HM facing acetate and propionate upgrading. • Acetate and propionate upgrading caused low δ13CH 4. How the acetate and propionate accumulation impact anaerobic syntrophy during methane formation is not well understood. To investigate such effect, continuous acetate (35 g/L), propionate (11.25 g/L) and bicarbonate (30 g/L) supplementation were used during mesophilic anaerobic digestion. The high throughput sequencing (16S rRNA and mcrA), Real-Time quantitative PCR, and stable carbon isotope fingerprinting were applied to investigate the structure and activity of microbial community members. The results demonstrated that the abundance of syntrophic acetate oxidizing bacteria exhibited a gradual decrease coupled with heavier stable carbon isotopic signature of methane (δ 13CH 4) in the three reagents impacted reactors. The increased acetate and propionate concentrations exerted negative influence on biogas production but the relatively stable hydrogenotrophic methanogens together with syntrophic acetate/propionate oxidizing bacteria kept the stable methane formation facing acetate and propionate accumulation. The functional genes copy number of the hydrogenotrophic Methanocellaceae and Methanomicrobiaceae correlated significantly with δ 13CH 4 (R2 > 0.74), but only the abundance of Methanocellaceae fitted well with δ 13CH 4 (p < 0.05). The δ 13CH 4 signatures can predict methanogenesis, as it directly reflects the main methanogenic pathway; yet, further investigation of isotope fractionation in acetate/propionate coupled with δ 13CH 4 is needed. Collectively, these results provide deep insight into anaerobic syntrophy and reveal changes of synergistic relationships, both of which may contribute to the stability of biogas reactors. [ABSTRACT FROM AUTHOR]

Bifidobacteria are one genus of low-abundance gut commensals that are often associated with host health-promoting effects. Bifidobacteria can degrade various dietary fibers (i.e., galactooligosaccharides, fructooligosaccharides, inulin), and are reported as one of the few gut-dwelling microbes that can utilize host-derived carbohydrates (mucin and human milk oligosaccharides). Previous studies have noted that the superior carbohydrate-metabolizing abilities of bifidobacteria facilitate the intestinal colonization of this genus and also benefit other gut symbionts, in particular butyrate-producing bacteria, via cooperative metabolic interactions. Given that such cross-feeding activities of bifidobacteria on mucin and oligosaccharides have not been systematically summarized, here we review the carbohydrate-degrading capabilities of various bifidobacterial strains that were identified in vitro experiments, the core enzymes involved in the degradation mechanisms, and social behavior between bifidobacteria and other intestinal microbes, as well as among species-specific bifidobacterial strains. The purpose of this review is to enhance our understanding of the interactions of prebiotics and probiotics, which sheds new light on the future use of oligosaccharides and bifidobacteria for nutritional intervention or clinical application. • Identify bifidobacterial capabilities in utilizing host-/diet-derived glycans. • Explore the core enzymes involved in glycan-harvesting mechanisms of bifidobacteria. • Summarize techniques are used to study cross-feeding activities by bifidobacteria. • Focus on the role of mucin and oligosaccharides via cross-feeding activities by Bifidobacterium. [ABSTRACT FROM AUTHOR]

Cells in assemblages differentiate and perform distinct roles. Though many pathways of differentiation are understood at the molecular level in multicellular eukaryotes, the elucidation of similar processes in bacterial assemblages is recent and ongoing. Here, we discuss examples of bacterial differentiation, focusing on cases in which distinct metabolisms coexist and those that exhibit cross-feeding, with one subpopulation producing substrates that are metabolized by a second subpopulation. We describe several studies of single-species systems, then segue to studies of multispecies metabolic heterogeneity and cross-feeding in the clinical setting. Many of the studies described exemplify the application of new techniques and modeling approaches that provide insights into metabolic interactions relevant for bacterial growth outside the laboratory. Metabolic diversification in bacterial systems arises from innate stochasticity and can be further promoted by growth in chemical gradients and/or constrained spaces. Metabolic heterogeneity can enable metabolite cross-feeding, and cross-feeding itself can promote the development of metabolically differentiated subpopulations. New techniques for characterizing metabolically diversified subpopulations in situ include those that incorporate three-dimensional dynamic flux balance analysis, 13C-metabolic flux analysis, growth in microfluidic devices, and stimulated Raman scattering microscopy. Metabolic heterogeneity is an important factor to incorporate into models of infection because it influences virulence and antibiotic susceptibility. [ABSTRACT FROM AUTHOR]

Nearly all microbes rely on other species in their environment to provide nutrients they are unable to produce. Nutritional interactions include not only the exchange of carbon and nitrogen compounds, but also amino acids and cofactors. Interactions involving cross-feeding of cobamides, the vitamin B 12 family of cofactors, have been developed as a model for nutritional interactions across species and environments. In addition to experimental studies, new developments in culture-independent methodologies such as genomics and modeling now enable the prediction of nutritional interactions in a broad range of organisms including those that cannot be cultured in the laboratory. New insights into the mechanisms and evolution of microbial nutritional interactions are beginning to emerge by combining experimental, genomic, and modeling approaches. [ABSTRACT FROM AUTHOR]

The gut microbiota, a complex and dynamic microbial ecosystem, plays a crucial role in regulating the intestinal barrier. Polysaccharide foraging is specifically dedicated to establishing and maintaining microbial communities, contributing to the shaping of the intestinal ecosystem and ultimately enhancing the integrity of the intestinal barrier. The utilization and regulation of individual polysaccharides often rely on distinct gut-colonizing bacteria. The products of their metabolism not only benefit the formation of the ecosystem but also facilitate cross-feeding partnerships. In this review, we elucidate the mechanisms by which specific bacteria degrade polysaccharides, and how polysaccharide metabolism shapes the microbial ecosystem through cross-feeding. Furthermore, we explore how selectively promoting microbial ecosystems and their metabolites contributes to improvements in the integrity of the intestinal barrier. [ABSTRACT FROM AUTHOR]

Under high ammonia stress, there remains limited understanding regarding the genetic and metabolic responses of key players within the high-sulfate wastewater treatment system. In this study, the influence of high ammonia concentrations (1000–2000 mg/L) on pollutants removal and microbial response in high-sulfate wastewater was investigated. Surprisingly, our study found a robust ammonia resilience, as demonstrated by the stable removal efficiencies of chemical oxygen demand (COD) at 60.64% and sulfate at 79.76%. The core functional bacteria, Desulfovibrio and Erysipelatoclostridium , responsible for sulfate and COD removal, were discovered to remain at a relative abundance of up to 47.61% and 40.22%, respectively. Metagenomic analysis showed that three bins assigned to Desulfovibrio contain genes encoding glucokinase (glk), phosphofohexokinase (PFK) and pyruvate kinase (PK), indicating their capability for complete carbon metabolism. Of significance, this study revealed a remarkable amount of gene up-regulation involved in sulfur metabolism, showing resilience against ammonia stress. Unexpectedly, a positive correlation (p < 0.05) was observed between genes (aroAC and trpABDFG) responsible for tryptophan biosynthesis and the relative abundance of Erysipelatoclostridium. The complete genetic pathway for tryptophan biosynthesis was uncovered in two bins associated with Erysipelatoclostridium , suggesting potential interspecies cross-feeding between Erysipelatoclostridium and Desulfovibrio for maintaining functional stability. Overall, the microbial collaboration from key players in the high-sulfate wastewater enhances the system's resilience to withstand ammonia stress, thereby contributing to the stability for treating high-sulfate wastewater. [Display omitted] • The sulfate reduction system exhibited a high resilience to ammonia stress (1000–2000 mg/L). • Desulfovibrio and Erysipelatoclostridium played key roles in sulfate and chemical oxygen demand removal. • Sulfur metabolism genes were significantly up-regulated under ammonia stress. • Erysipelatoclostridium was a potential contributor to tryptophan production within the sulfate-reducing system. • Cross-feeding between Erysipelatoclostridium and Desulfovibrio was favorable for maintaining functional stability. [ABSTRACT FROM AUTHOR]

To explore the feasibility of biofilter reactor to treat municipal secondary effluent deeply without extra carbon source, this paper proposed an integrated biofilter reactor (IBFR) coupling partial denitrification (PD) with anammox (A) to treat the secondary effluent and raw sewage with the flow ratio of 3:1 together. The results show that the effluent concentration of TN and COD in IBFR could be reduced to 10 mg/L and 15 mg/L, respectively, under hydraulic retention time of 1.5 h and nitrogen loading rate of 0.55 kg/(m3·d). The highest specific anammox activity (19.2 mg N/(g TVS·d)) and the maximum extracellular polymeric substance (EPS) content (107.21 mg/g TVS) occurred at the 25–50 cm section of IBFR, where Thauera , Candidatus Anammoximicrobium and Candidatus Brocadia were the dominant denitrifiers and anammox bacteria. Furthermore, the cyclic self-stratification occurred along the reactor height, where the utilization, decomposition, transformation and cross-feeding of EPS enhanced the performance stability of nitrogen and carbon removal, strengthened the niche structure and promoted the synergistic symbiosis. In conclusion, IBFR coupling PD and A demonstrated the possibility to treat secondary effluent without additional carbon sources, which is expected as an alternative approach for tertiary treatment of municipal wastewater. [Display omitted] • Tertiary purification was achieved in IBFR by PD and AMX without extra carbon source. • PD and AMX adapted to poor substrate stress through synergistic symbiosis strategy. • Cyclic self-stratification along the height was the niche feature in IBFR. • Microbial cross-feeding in IBFR was based on using, decomposing and transforming EPS. [ABSTRACT FROM AUTHOR]

The chain elongation bioprocess for the production of medium-chain carboxylates (MCCs) is promising for resource recovery from organic wastes. In this study, the microbiome development and metabolic interactions in chain elongation system with 10% granular activated carbon (GAC, size between 1.5–2 mm) were investigated. The bioreactor achieved an electron recovery rate over 70%, and the carbon distribution towards caproate was over 64%. Additionally, the microbial community structure shifted and chain elongation microbiome rapidly acclimated from traditional anaerobic fermentation consortia. The taxonomic composition shifted in favor of MCCs production by enriching the key microbes associated with caproate production. Caproate-producing Clostridium (75% abundance) and proteolytic Proteiniphilum remarkably predominated in the microbial community. Further metagenomics analysis recovered genome bins of Clostridium kluyveri , Clostrium indolis , Clostridium aminovalericum and Proteiniclasticum ruminis , which together represented the majority of the microbial community. Among them, the complete ethanol-acetate fermentation for caproate production via the reversed β-oxidation pathway (RBO) and fatty acid biosynthesis (FAB) pathway were fully recovered, suggesting that both the pathways contributed to MCCs formation. Further metabolic pathways analysis suggested that microbial metabolic exchanges between chain elongator and symbiotic bacteria, such as cross-feeding of acetate and acetyl-CoA, is vital to shape a robust microbial ecosystem. • GAC enhanced MCCs formation with an electron recovery rate over 70%. • The carbon distribution towards caproate reached 64%. • Microbial taxonomic composition shifted in favor of the production of MCCs. • Both reversed β-oxidation and fatty acid biosynthesis pathways contributed to MCCs formation. • Cross-feeding between chain elongator and symbiotic bacteria is vital to the ecosystem. [ABSTRACT FROM AUTHOR]

[Display omitted] • A consortium proficient in TAP degradation was domesticated from activated sludge. • TAP metabolic fate, mechanism and cross-feeding were first unraveled by muti-omics. • Key species Hydrogenophaga and Bosea inactivated TAP by oxidation and acetylation. • Hydrogenophaga sp. stored carbon and nitrogen by synthesizing cyanophycin and PHB. Thiamphenicol (TAP), a typical veterinary antibiotic, is emerging as a contaminant in livestock, poultry, and aquaculture environments. Addressing this concern, this study domesticated a TAP-degrading consortium in a lab-scale activated sludge bioreactor, demonstrating efficient degradation of up to 200 mg/L TAP within 50 h and elimination of antimicrobial activity. The microbial compositions, cross-feeding interactions, and underlying metabolic mechanisms were unveiled through multi-omics. TAP was modified at two hydroxyl groups for the initial step in three pathways including oxidation at C 3 -OH, dehydrogenation at both C 1 -OH and C 3 -OH, and acetylation at C 3 -OH. Hydrogenophaga (MAG1 and MAG2) and Bosea (MAG9) were implicated in oxidation and acetylation of TAP, respectively. Aromatic compounds and 2,2-dichloroacetic acid (DCA) were the principal downstream metabolites of TAP. MAG9 (Bosea), MAG10 (Rubrivivax), and MAG13 (Hyphomicrobium) were predicted as DCA degraders, while MAG4 (Xanthobacteraceae, Ga0077548) and MAG10 (Rubrivivax) conducted the catabolism of aromatic compounds. Therefore, consortium members collaborated to efficiently reduce and detoxify TAP. Furthermore, the co-metabolism of TAP and extracellular substrates supported the microbial populations' growth. Genomic traits and transcriptional profiles suggested that the dominant Hydrogenophaga (MAG1) could store carbon and nitrogen by synthesizing cyanophycin and polyhydroxybutyrate biopolymers. Ultimately, this comprehensive understanding of TAP biodegradation will aid in formulating efficient biotreatment strategies for TAP-contaminated environments. [ABSTRACT FROM AUTHOR]

[Display omitted] • BioH 2 yield increased by 65.2% with adding Geobacter metallireducens culture (GM) • Extracellular polymeric substances (EPS) of GM helped to promote bioH 2 production. • c-Cyts were identified as key electroactive functional components in the EPS of GM. • Hydrogenase activity, ETS activity and NADH/NAD+ ratio were enhanced by adding GM. • Interspecies electron syntrophy enriched bioH 2 producer Clostridium sensu stricto. To modulate the electron transfer behavior of hydrogen-producing bacteria (HPB) for enhanced hydrogen production, Geobacter metallireducens culture (GM) was introduced as an electron syntrophy partner and redox balance regulator in dark fermentation systems with hydrogen-producing sludge (HPS) as inoculum. The highest hydrogen yield was 306.5 mL/g-COD at the GM/HPS volatile solids ratio of 0.08, which was 65.2 % higher than the HPS group. The multi-layered extracellular polymeric substances (EPS) of GM played a significant role in promoting hydrogen production, with c-type cytochromes probably serving as electroactive functional components. The addition of GM significantly improved the NADH/NAD+ ratio, electron transport system activity, hydrogenase activity, and electrochemical properties of HPS. Furthermore, the microbial community structure and metabolic functions were optimized due to the potential syntrophic interaction between Clostridium sensu stricto (dominant HPB) and Geobacter , thus promoting hydrogen production. This study provided novel insights into the interactions among exoelectrogens , electroactive EPS, and mixed HPB. [ABSTRACT FROM AUTHOR]

[Display omitted] • Electron repulsion-weak and redox groups-rich GAC surface favored anammox enrichment. • GAC reinforced EPS synthesis and secretion to construct anammox protective layer. • GAC spurred high basal metabolic activity to expedite starved anammox rejuvenation. • GAC facilitated anammox consortia co-metabolism to form diverse metabolic circuits. This article investigates the buffering capacity and recovery-enhancing ability of granular activated carbon (GAC) in a starved (influent total nitrogen: 20 mg/L) anaerobic ammonium oxidation (anammox) reactor. The findings revealed that anammox aggregated and sustained basal metabolism with shorter performance recovery lag (6 days) and better nitrogen removal efficiency (84.9 %) due to weak electron-repulsion and abundance redox-active groups on GAC's surface. GAC-supported enhanced extracellular polymeric substance secretion aided anammox in resisting starvation. GAC also facilitated anammox bacterial proliferation and expedited the restoration of anammox microbial community from a starved state to its initial-level. Metabolic function analyses unveiled that GAC improved the expression of genes involved in amino acid metabolism and sugar-nucleotide biosynthesis while promoted microbial cross-feeding, ultimately indicating the superior potential of GAC in stimulating more diverse metabolic networks in nutrient-depleted anammox consortia. This research sheds light on the microbial and metabolic mechanisms underlying GAC-mediated anammox system in low-substrate habitats. [ABSTRACT FROM AUTHOR]

An integrative pattern-process-mechanism approach is revealing the roles of biotic interactions in microbiome assembly. Patterns of microbiome diversity observed in metagenomic studies can be partly explained by interaction processes (e.g. competition, facilitation) and underlying molecular or genetic mechanisms (e.g. antibiotic production, nutrient cross-feeding). Exciting opportunities remain to fully understand the significance and generalizability of biotic interactions within microbiomes. Many microbial interactions have been studied by chasing easily quantifiable phenotypes including changes in growth or pigmentation, but it is likely that diverse cryptic interactions occur without obvious growth changes or macroscopic phenotypes. A narrow phylogenetic breadth of well-studied microbes limits our understanding of whether there are conserved genetic or molecular mechanisms of microbial interactions. Biotic interactions can impose strong selective pressures that could shape rates and modes of microbial evolution, but few studies have examined the evolutionary consequences of interactions within microbiomes. Continued exploration of the chemical and genetic mechanisms underlying biotic interactions may provide novel tools to manipulate and manage microbiomes. [ABSTRACT FROM AUTHOR]

Microbial interactions play an important role in regulating the metabolic function of fermented food communities, especially the production of key flavor compounds. However, little is known about specific molecular mechanisms that regulate the production of key flavor compounds through microbial interactions. Here, we designed a synthetic consortium containing Debaryomyces hansenii D1, Staphylococcus xylosus S1, and Pediococcus pentosaceus PP1 to explore the mechanism of the microbial interactions underlying the branched-chain aldehydes production. In this consortium, firstly, D. hansenii secreted amino acids that promoted the growth of P. pentosaceus and S. xylosus. Specifically, D. hansenii D1 secreted alanine, aspartate, glutamate, glutamine, glycine, phenylalanine, serine, and threonine, which were the primary nutrients for bacterial growth. P. pentosaceus PP1 utilized all these eight amino acids through cross-feeding, whereas S. xylosus S1 did not utilize aspartate and serine. Furthermore, D. hansenii D1 promoted the production of branched-chain aldehydes from S. xylosus and P. pentosaceus through cross-feeding of α-keto acids (intermediate metabolites). Thus, the accumulation of 2-methyl-butanal was promoted in all co-culture. Overall, this work revealed the mechanism by which D. hansenii and bacteria cross-feed to produce branched-chain aldehydes in fermented sausages. • There is cross-feeding of amino acids and α-keto acids between S. xylosus S1 and P. pentosaceus PP1 with D. hansenii D1. • The amino acids provided by D. hansenii D1 are the primary growth-promoting nutrients of bacterial growth. • The co-culture of D. hansenii D1 and bacteria enhanced branched chain aldehydes production by α-keto acids cross-feeding. • D. hansenii D1 could convert branched-chain aldehydes, especially 3-methyl-butanal, to the corresponding alcohols. [ABSTRACT FROM AUTHOR]

Although partial denitrification coupled with the anammox process has received considerable attention, the partial denitrification function of companion bacteria in mixotrophic anammox systems remains experimentally investigated. Herein, a partial denitrification process was realized in mixotrophic anammox systems with a COD/TN ratio of 0.75. Furthermore, the experimental verification results revealed that nitrate and ammonia were eliminated concurrently, showing that partial denitrifying bacteria were present in the mixotrophic anammox systems. Denitratisoma and Norank Xanthobacteraceae were the dominant genera of companion bacteria containing functional genes related to partial denitrification. Especially, Denitratisoma was a companion bifunctional bacterium for Candidatus Kuenenia shifted between complete and partial denitrification at different COD/TN ratios. Moreover, nir gene abundance in the mixotrophic anammox system increased by 135.4 % compared to that in the autotrophic anammox system. In contrast, nor gene abundance decreased by 28.00 %, indicating that NO might be used as a medium for cross-feeding anammox and partial denitrification. This study provides a more thorough understanding of companion bacteria in mixotrophic anammox systems. [Display omitted] • Companion partial denitrifying bacteria existed in mixotrophic anammox systems. • Removal efficiency of TN was 98.91 ± 0.60 % with a COD/TN ratio of 0.75. • Norank Xanthobacteraceae was a dominant genus related to partial denitrification. • Denitratisoma was a companion bifunctional bacterium for Candidatus Kuenenia. • Partial denitrifying bacteria exhibited NO cross-feeding with anammox bacteria. [ABSTRACT FROM AUTHOR]

[Display omitted] • Reactor performance was independent of the relative abundance of anammox bacteria. • The overall migration of microbes from flocs to biofilm was verified. • Microbial interactions were vital to sludge proliferation and biofilm formation. • Acetate and glycogen produced by AnAOB act as key substrates for cross-feeding. Two mature anaerobic ammonium oxidation (anammox) consortia with high/low relative abundance of anammox bacteria were inoculated for the rapid sludge proliferation and biofilm formation in this study, named up-flow anaerobic sludge blanket reactor (UASB1) (high) and UASB2 (low), respectively. Results showed that the nitrogen removal efficiency of UASB2 reached 90.94% after the 120-day operation, which was 13% higher than that of UASB1. Moreover, its biomass amounts were 22.18% (biofilm) and 40.96% (flocs) higher than that of UASB1, respectively. Ca. Kuenenia possessed relative abundances of 29.32% (flocs), 27.42% (biofilm) and 31.56% (flocs), 35.20% (biofilm) in the UASB1 and UASB2, respectively. The relative abundances of genes involved in anammox transformation (hzs , nir) and carbon metabolism (fdh , lgA/B/C , acs) were higher in the UASB2, indicating that Ca. Kuenenia might produce acetate and glycogen to enhance microbial interactions. These findings emphasized the importance of microbial interactions in anammox sludge proliferation and biofilm formation. [ABSTRACT FROM AUTHOR]

Bicarbonate (HCO 3 − ) has been extensively researched as a buffer in anaerobic digestion. The effect of HCO 3 − concentration on syntrophic butyrate oxidation process was evaluated by batch culturing of anaerobic activated sludge, and the mechanism was further revealed by the changes of Gibbs free energy (Δ G ) and the interspecies transfers of electron and proton. The results showed that butyrate degradation rate was enhanced by 32.07% when the supplement of HCO 3 − increased from 0 to 0.20 mol/L. However, methane production and acetate degradation were strongly inhibited by HCO 3 − more than 0.10 mol/L. More function of HCO 3 − was found as 1) decreasing the Δ G of syntrophic methanogenesis of butyrate while increasing the Δ G of methanogenesis of acetate, 2) enriching M. harundinacea and M. concilii , 3) increasing the diffusion rate of protons between the syntrophic consortia. This work would increase the anaerobic digestion efficiency by enhancing the interaction of the syntrophic consortia. [ABSTRACT FROM AUTHOR]

Bifidobacteria represent one of the first colonizers of the mammalian gut, where such colonization is facilitated by their saccharolytic capabilities. Genomic analyses of bifidobacteria have revealed intriguing genetic strategies employed by these bacteria to access a variety of dietary and host-produced glycans. Bifidobacterial genome evolution therefore represents a fascinating example of how their chromosomes were molded to contain a large number of genes involved in carbohydrate metabolism. One of the reasons as to why bifidobacteria are such dominant and prevalent members of the (early) microbiota is that they may access glycans in the gut through mutualistic cross-feeding or resource-sharing activities, which is indicative of ‘social behavior’ among bifidobacterial strains. [ABSTRACT FROM AUTHOR]

Granule-based partial denitrification and anammox (PDA) process is affected by microbial community. To reveal how the nitrogen conversion rate varies with microbial composition caused by the granule size, PDA granules were divided into five sizes (<0.2, 0.2–0.5, 0.5–0.9, 0.9–1.6, and 1.6–2.0 mm). The abundance of anammox bacteria (dominated by Candidatus Brocadia) increased with particle size and peaked at 14.6% for 0.9–1.6 mm. In contrast, the abundance of denitrifiers (dominated by Thauera) decreased from 83.3% to 23.5% when granule size increased from <0.2 mm to 0.5–0.9 mm, but increased to 48.1% with further increases in particle size to 1.6–2.0 mm. The nitrogen conversion rate was affected by the microbial composition in granules. Nitrogen was autonomously removed in the granules of 0.9–2.0 mm. However, nitrite was accumulated in granules of <0.9 mm. Nitrite cross-feeding occurred inside and between granules. The findings provide a reference for the regulation of granule-based PDA systems. [Display omitted] • Enhanced nitrogen removal and forming PDA granular sludge were achieved. • Microbial community of PDA granular sludge is affected by particle size. • Nitrogen conversion rate of granular sludge is affected by microbial community. • Nitrite cross-feeding occurred inside and between PDA granules. • A regulation strategy was proposed for optimizing the efficiency of PDA system. [ABSTRACT FROM AUTHOR]

[Display omitted] • Xylan consumption was led by Bacteroides species. • Xylan degradation by Bacteroides ovatus allowed Bifidobacterium longum growth. • Proteomics studies showed sugars cross-feeding between B. ovatus and B. longum. The intestinal microbiome is a community of anaerobic microorganisms whose activities significantly impact human health. Its composition can be modulated by consuming foods rich in dietary fiber, such as xylan, a complex polysaccharide that can be considered an emerging prebiotic. In this work, we evaluated how certain gut bacteria acted as primary degraders, fermenting dietary fibers, and releasing metabolites that other bacteria can further use. Different bacterial strains of Lactobacillus , Bifidobacterium , and Bacteroides were evaluated for their ability to consume xylan and interact with one another. Results from unidirectional assays gave indications of possible cross-feeding between bacteria using xylan as a carbon source. Bidirectional assays showed that Bifidobacterium longum PT4 increased its growth in the presence of Bacteroides ovatus HM222. Proteomic analyses indicated that B. ovatus HM222 synthesizes enzymes facilitating xylan degradation, such as β-xylanase, arabinosidase, L-arabinose isomerase, and xylosidase. Interestingly, the relative abundance of these proteins remains largely unaffected in the presence of Bifidobacterium longum PT4. In the presence of B. ovatus , B. longum PT4 increased the production of enzymes such as α-L-arabinosidase, L-arabinose isomerase, xylulose kinase, xylose isomerase, and sugar transporters. These results show an example of positive interaction between bacteria mediated by xylan consumption. Bacteroides degraded this substrate to release xylooligosaccharides, or monosaccharides (xylose, arabinose), which might support the growth of secondary degraders such as B. longum. [ABSTRACT FROM AUTHOR]

Recent findings have shaken our picture of the biology of the archaea and revealed novel traits beyond archaeal extremophily and supposed ‘primitiveness’. The archaea constitute a considerable fraction of the Earth’s ecosystems, and their potential to shape their surroundings by a profound interaction with their biotic and abiotic environment has been recognized. Moreover, archaea have been identified as a substantial component, or even as keystone species, in complex microbiomes – in the environment or accompanying a holobiont. Species of the Euryarchaeota (methanogens, halophiles) and Thaumarchaeota, in particular, have the capacity to coexist in plant, animal, and human microbiomes, where syntrophy allows them to thrive under energy-deficiency stress. Due to methodological limitations, the archaeome remains mysterious, and many questions with respect to potential pathogenicity, function, and structural interactions with their host and other microorganisms remain. [ABSTRACT FROM AUTHOR]

Direct interspecies electron transfer (DIET) is a recently discovered microbial syntrophy where cell-to-cell electron transfer occurs between syntrophic microbial species. DIET between bacteria and methanogenic archaea in anaerobic digestion can accelerate the syntrophic conversion of various reduced organic compounds to methane. DIET-based syntrophy can naturally occur in some anaerobic digester via conductive pili, however, can be engineered via the addition of various non-biological conductive materials. In recent years, research into understanding and engineering DIET-based syntrophy has emerged with the aim of improving methanogenesis kinetics in anaerobic digestion. This article presents a state-of-art review focusing on the fundamental mechanisms, key microbial players, the role of electrical conductivity, the effectiveness of various conductive additives, the significance of substrate characteristics and organic loading rates in promoting DIET in anaerobic digestion. [ABSTRACT FROM AUTHOR]

Anaerobic hydrocarbon biodegradation not only diminishes fuel quality, but also exacerbates the biocorrosion of the metallic infrastructure. While successional events in marine microbial ecosystems impacted by petroleum are well documented, far less is known about the response of communities chronically exposed to hydrocarbons. Shipboard oily wastewater was used to assess the biotransformation of different diesel fuels and their propensity to impact carbon steel corrosion. When amended with sulfate and an F76 military diesel fuel, the sulfate removal rate in the assay mixtures was elevated (26.8 μM/d) relative to incubations receiving a hydroprocessed biofuel (16.1 μM/d) or a fuel-unamended control (17.8 μM/d). Microbial community analysis revealed the predominance of Anaerolineae and Deltaproteobacteria in F76-amended incubations, in contrast to the Beta- and Gammaproteobacteria in the original wastewater. The dominant Smithella- like sequences suggested the potential for syntrophic hydrocarbon metabolism. The general corrosion rate was relatively low (0.83 − 1.29 ± 0.12 mpy) and independent of the particular fuel, but pitting corrosion was more pronounced in F76-amended incubations. Desulfovibrionaceae constituted 50–77% of the sessile organisms on carbon steel coupons. Thus, chronically exposed microflora in oily wastewater were differentially acclimated to the syntrophic metabolism of traditional hydrocarbons but tended to resist isoalkane-laden biofuels. [ABSTRACT FROM AUTHOR]