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Understanding how microorganism-microorganism interactions shape microbial assemblages is a key to deciphering the evolution of dependencies and co-existence in complex microbiomes. Metabolic dependencies in cross-feeding exist in microbial communities and can at least partially determine microbial community composition. To parry the complexity and experimental limitations caused by the large number of possible interactions, new concepts from systems biology aim to decipher how the components of a system interact with each other. The idea that cross-feeding does impact microbiome assemblages has developed both theoretically and empirically, following a systems biology framework applied to microbial communities, formalized as microbial systems ecology (MSE) and relying on integrated-omics data. This framework merges cellular and community scales and offers new avenues to untangle microbial coexistence primarily by metabolic modeling, one of the main approaches used for mechanistic studies. In this mini-review, we first give a concise explanation of microbial cross-feeding. We then discuss how MSE can enable progress in microbial research. Finally, we provide an overview of a MSE framework mostly based on genome-scale metabolic-network reconstruction that combines top-down and bottom-up approaches to assess the molecular mechanisms of deterministic processes of microbial community assembly that is particularly suitable for use in synthetic biology and microbiome engineering. [ABSTRACT FROM AUTHOR]

Spacecraft attitude and orbit estimation are considered very important tasks for nearly every spacecraft. The full state estimation process is usually done using the Extended Kalman Filter (EKF). Nonlinearities associated with spacecraft model, measurement model, and disturbance models represent a serious obstacle for EKF to be implemented on-board a spacecraft. In order to overcome this problem, two neural networks architecture are developed. They are the direct architecture and the cross-feeding architecture. The first one can estimate the spacecraft orbital states but it has a degraded accuracy for the spacecraft representing attitude states. A modification of the direct architecture is made to enable simultaneous estimation of spacecraft attitude and orbit states and named as cross-feeding architecture. The cross-feeding architecture has outperformed the EKF. It has the same accuracy as the EKF, with less than half of its execution time. An EKF is used to provide data set for training and validation of the neural networks solution. In order to avoid overfitting and enhance network generalization, 15% of the EKF data set is used to validate the solution. The developed algorithms have the ability to deal with initial high estimation errors without using any small angle approximation. Thus, the developed algorithms can work in all the spacecraft operational modes. [ABSTRACT FROM AUTHOR]

Microbial species occupying the same ecological niche or codeveloping during a fermentation process can exchange metabolites and mutualistically influence each other's metabolic states. For instance, yeast can excrete amino acids, thereby cross-feeding lactic acid bacteria unable to grow without an external amino acid supply. The yeast membrane transporters involved in amino acid excretion remain poorly known. Using a yeast mutant overproducing and excreting threonine (Thr) and its precursor homoserine (Hom), we show that excretion of both amino acids involves the Aqr1, Qdr2, and Qdr3 proteins of the Drug H+-Antiporter Family (DHA1) family. We further investigated Aqr1 as a representative of these closely related amino acid exporters. In particular, structural modeling and molecular docking coupled to mutagenesis experiments and excretion assays enabled us to identify residues in the Aqr1 substrate-binding pocket that are crucial for Thr and/or Hom export. We then co-cultivated yeast and Lactobacillus fermentum in an amino-acid-free medium and found a yeast mutant lacking Aqr1, Qdr2, and Qdr3 to display a reduced ability to sustain the growth of this lactic acid bacterium, a phenotype not observed with strains lacking only one of these transporters. This study highlights the importance of yeast DHA1 transporters in amino acid excretion and mutualistic interaction with lactic acid bacteria. [ABSTRACT FROM AUTHOR]

Child undernutrition is a global health issue associated with a high burden of infectious disease. Undernourished children display an overabundance of intestinal pathogens and pathobionts, and these bacteria induce enteric dysfunction in undernourished mice; however, the cause of their overgrowth remains poorly defined. Here, we show that disease-inducing human isolates of Enterobacteriaceae and Bacteroidales spp. are capable of multi-species symbiotic cross-feeding, resulting in synergistic growth of a mixed community in vitro. Growth synergy occurs uniquely under malnourished conditions limited in protein and iron: in this context, Bacteroidales spp. liberate diet- and mucin-derived sugars and Enterobacteriaceae spp. enhance the bioavailability of iron. Analysis of human microbiota datasets reveals that Bacteroidaceae and Enterobacteriaceae are strongly correlated in undernourished children, but not in adequately nourished children, consistent with a diet-dependent growth synergy in the human gut. Together these data suggest that dietary cross-feeding fuels the overgrowth of pathobionts in undernutrition. Malnourished children experience a high burden of intestinal pathogens that exacerbate growth stunting, and preventing this pathogen overgrowth has proved challenging. Here the authors show that diet-specific bacterial crossfeeding contributes to the overgrowth of intestinal pathogens during child malnutrition. [ABSTRACT FROM AUTHOR]

Bacteria commonly live in spatially structured biofilm assemblages, which are encased by an extracellular matrix. Metabolic activity of the cells inside biofilms causes gradients in local environmental conditions, which leads to the emergence of physiologically differentiated subpopulations. Information about the properties and spatial arrangement of such metabolic subpopulations, as well as their interaction strength and interaction length scales are lacking, even for model systems like Escherichia coli colony biofilms grown on agar-solidified media. Here, we use an unbiased approach, based on temporal and spatial transcriptome and metabolome data acquired during E. coli colony biofilm growth, to study the spatial organization of metabolism. We discovered that alanine displays a unique pattern among amino acids and that alanine metabolism is spatially and temporally heterogeneous. At the anoxic base of the colony, where carbon and nitrogen sources are abundant, cells secrete alanine via the transporter AlaE. In contrast, cells utilize alanine as a carbon and nitrogen source in the oxic nutrient-deprived region at the colony mid-height, via the enzymes DadA and DadX. This spatially structured alanine cross-feeding influences cellular viability and growth in the cross-feeding-dependent region, which shapes the overall colony morphology. More generally, our results on this precisely controllable biofilm model system demonstrate a remarkable spatiotemporal complexity of metabolism in biofilms. A better characterization of the spatiotemporal metabolic heterogeneities and dependencies is essential for understanding the physiology, architecture, and function of biofilms. [ABSTRACT FROM AUTHOR]

New microbial communities often arise through the mixing of two or more separately assembled parent communities, a phenomenon that has been termed "community coalescence". Understanding how the interaction structures of complex parent communities determine the outcomes of coalescence events is an important challenge. While recent work has begun to elucidate the role of competition in coalescence, that of cooperation, a key interaction type commonly seen in microbial communities, is still largely unknown. Here, using a general consumer-resource model, we study the combined effects of competitive and cooperative interactions on the outcomes of coalescence events. To do so, we simulate coalescence events between pairs of communities with different degrees of competition for shared carbon resources and cooperation through cross-feeding on leaked metabolic by-products (facilitation). We also study how structural and functional properties of post-coalescence communities evolve when they are subjected to repeated coalescence events. We find that in coalescence events, the less competitive and more cooperative parent communities contribute a higher proportion of species to the new community because this endows superior ability to deplete resources and resist invasions. Consequently, when a community is subjected to repeated coalescence events, it gradually evolves towards being less competitive and more cooperative, as well as more speciose, robust and efficient in resource use. Encounters between microbial communities are becoming increasingly frequent as a result of anthropogenic environmental change, and there is great interest in how the coalescence of microbial communities affects environmental and human health. Our study provides new insights into the mechanisms behind microbial community coalescence, and a framework to predict outcomes based on the interaction structures of parent communities. Author summary: In nature, new microbial communities often arise from the fusion of whole, previously separate communities (community coalescence). Despite the crucial role that interactions among microbes play in the dynamics of complex communities, our ability to predict how these affect the outcomes of coalescence events remains limited. Here, using a general mathematical model, we study how the structure of species interactions confers an advantage upon a microbial community when it encounters another, and how communities evolve after undergoing repeated coalescence events. We find that competitive interactions between species preclude their survival upon a coalescence event, while cooperative interactions are advantageous for post-coalescence survival. Furthermore, after a community is exposed to many coalescence events, the remaining species become less competitive and more cooperative. Ultimately, this drives the community evolution, yielding post-coalescence communities that are more species-rich, productive, and resistant to invasions. There are many potential environmental and health implications of microbial community coalescence, which will benefit from the theoretical insights that we offer here about the fundamental mechanisms underlying this phenomenon. [ABSTRACT FROM AUTHOR]

Methane-oxidizing bacteria (methanotrophs) often coexist with methylotrophs that utilize methanol excreted by methanotrophs. Recently, we found that a facultative methylotroph, Methyloceanibacter caenitepidi Gela4T, possibly utilizes acetate rather than methanol in the coculture with a methanotroph, Methylocaldum marinum S8. Here, we examined the effects of oxygen concentrations on growth of and acetate excretion by M. marinum S8 in pure culture and the coculture with M. caenitepidi Gela4T. M. marinum S8 excreted acetate during the exponential growth phase not only under microaerobic (O2 concentrations of 3.5%-6%) but also under aerobic (O2 concentrations of 20%-31%) conditions. RNA-Seq analyses of M. marinum S8 cells grown under aerobic conditions suggested that phosphoketolase and acetate kinase were candidate genes involved in acetate production. Nonmethylotrophic bacteria, Cupriavidus necator NBRC 102504, could grow when cocultured with M. marinum S8, also supporting the existence of methanol-independent cross-feeding from M. marinum S8 under aerobic conditions. Acetate excretion by Methylocaldum marinum S8 and methanol-independent cross-feeding between strain S8 and Methyloceanibacter caenitepidi Gela4T occurred under both aerobic and microaerobic conditions. [ABSTRACT FROM AUTHOR]

Summary: In the surface waters of the warm oligotrophic ocean, filaments and aggregated colonies of the nitrogen (N)‐fixing cyanobacterium Trichodesmium create microscale nutrient‐rich oases. These hotspots fuel primary productivity and harbour a diverse consortium of heterotrophs. Interactions with associated microbiota can affect the physiology of Trichodesmium, often in ways that have been predicted to support its growth. Recently, it was found that trimethylamine (TMA), a globally abundant organic N compound, inhibits N2 fixation in cultures of Trichodesmium without impairing growth rate, suggesting that Trichodesmium can use TMA as an alternate N source. In this study, 15N‐TMA DNA stable isotope probing (SIP) of a Trichodesmium enrichment was employed to further investigate TMA metabolism and determine whether TMA‐N is incorporated directly or secondarily via cross‐feeding facilitated by microbial associates. Herein, we identify two members of the marine Roseobacter clade (MRC) of Alphaproteobacteria as the likely metabolizers of TMA and provide genomic evidence that they converted TMA into a more readily available form of N, e.g., ammonium (NH4+), which was subsequently used by Trichodesmium and the rest of the community. The results implicate microbiome‐mediated carbon (C) and N transformations in modulating N2 fixation and thus highlight the involvement of host‐associated heterotrophs in global biogeochemical cycling. [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]

Quorum sensing (QS) offers cell density dependent dynamic regulations in cell culture through devices such as synchronized lysis circuit (SLC) and metabolic toggle switch (MTS). However, there is still a lack of studies on cocultivation with a combination of different QS-based devices. Taking the production of isopropanol and salidroside as case studies, we have mathematically modeled a comprehensive set of QS-regulated cocultivation schemes and constructed experimental combinations of QS devices, respectively, to evaluate their feasibility and optimality for regulating growth competition and corporative production. Glucose split ratio is proposed for the analysis of competition between cell growth and targeted production. Results show that the combination of different QS devices across multiple members offers a new tool with the potential to effectively coordinate synthetic microbial consortia for achieving high product titer in cross-feeding cocultivation. It is also evident that the performance of such systems is significantly affected by dynamic characteristics of chosen QS devices, carbon source control and the operational settings. This study offers insights for future applications of combinational QS devices in synthetic microbial consortia. • Dynamic regulation combining QS-SLC and QS-MTS proposed for cocultivation. • Glucose split ratio characterizes trade-off between cell growth and production. • Optimality of QS-SLC and QS-MTS schemes assessed. • Combinational QS devices used for balancing species and salidroside titer improvement. [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]

Background: A bacterial consortium SCP comprising three bacterial members, viz. Stenotrophomonas acidaminiphila APG1, Pseudomonas stutzeri APG2 and Cellulomonas sp. APG4 was developed for degradation of the mono-azo dye, Reactive Blue 28. The genomic analysis of each member of the SCP consortium was done to elucidate the catabolic potential and role of the individual organism in dye degradation. Results: The genes for glycerol utilization were detected in the genomes of APG2 and APG4, which corroborated with their ability to grow on a minimal medium containing glycerol as the sole co-substrate. The genes for azoreductase were identified in the genomes of APG2 and APG4, while no such trait could be determined in APG1. In addition to co-substrate oxidation and dye reduction, several other cellular functions like chemotaxis, signal transduction, stress-tolerance, repair mechanisms, aromatic degradation, and copper tolerance associated with dye degradation were also annotated. A model for azo dye degradation is postulated, representing the predominant role of APG4 and APG2 in dye metabolism while suggesting an accessory role of APG1. Conclusions: This exploratory study is the first-ever attempt to divulge the genetic basis of azo-dye co-metabolism by cross-genome comparisons and can be harnessed as an example for demonstrating microbial syntrophy. [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]

There is an increasing interest in the use of N2-fixing bacteria for the sustainable biofertilization of crops. Genetically-optimized bacteria for ammonium release have an improved biofertilization capacity. Some of these strains also cross-feed ammonium into microalgae raising additional concerns on their sustainable use in agriculture due to the potential risk of producing a higher and longer-lasting eutrophication problem than synthetic N-fertilizers. Here we studied the dynamic algal cross-feeding properties of a genetically-modified Azotobacter vinelandii strain which can be tuned to over-accumulate different levels of glutamine synthetase (GS, EC 6.3.1.20) under the control of an exogenous inducer. After switching cells overaccumulating GS into a noninducing medium, they proliferated for several generations at the expense of the previously accumulated GS. Further dilution of GS by cell division slowed-down growth, promoted ammonium-excretion and cross-fed algae. The final bacterial population, and timing and magnitude of algal N-biofertlization was finely tuned in a deferred manner. This tuning was in accordance with the intensity of the previous induction of GS accumulation in the cells. This bacterial population behavior could be maintained up to about 15 bacterial cell generations, until faster-growing and nonammonium excreting cells arose at an apparent high frequency. Further improvements of this genetic engineering strategy might help to align efficiency of N-biofertilizers and safe use in an open environment. Key points: • Ammonium-excreting bacteria are potential eutrophication agents • GS-dependent deferred control of bacterial growth and ammonium release • Strong but transient ammonium cross-feeding of microalgae [ABSTRACT FROM AUTHOR]

Background: Xylitol, a white or transparent polyol or sugar alcohol, is digestible by colonic microorganisms and promotes the proliferation of beneficial bacteria and the production of short-chain fatty acids (SCFAs), but the mechanism underlying these effects remains unknown. We studied mice fed with 0%, 2% (2.17 g/kg/day), or 5% (5.42 g/kg/day) (weight/weight) xylitol in their chow for 3 months. In addition to the in vivo digestion experiments in mice, 3% (weight/volume) (0.27 g/kg/day for a human being) xylitol was added to a colon simulation system (CDMN) for 7 days. We performed 16S rRNA sequencing, beneficial metabolism biomarker quantification, metabolome, and metatranscriptome analyses to investigate the prebiotic mechanism of xylitol. The representative bacteria related to xylitol digestion were selected for single cultivation and co-culture of two and three bacteria to explore the microbial digestion and utilization of xylitol in media with glucose, xylitol, mixed carbon sources, or no-carbon sources. Besides, the mechanisms underlying the shift in the microbial composition and SCFAs were explored in molecular contexts. Results: In both in vivo and in vitro experiments, we found that xylitol did not significantly influence the structure of the gut microbiome. However, it increased all SCFAs, especially propionate in the lumen and butyrate in the mucosa, with a shift in its corresponding bacteria in vitro. Cross-feeding, a relationship in which one organism consumes metabolites excreted by the other, was observed among Lactobacillus reuteri, Bacteroides fragilis, and Escherichia coli in the utilization of xylitol. At the molecular level, we revealed that xylitol dehydrogenase (EC 1.1.1.14), xylulokinase (EC 2.7.1.17), and xylulose phosphate isomerase (EC 5.1.3.1) were key enzymes in xylitol metabolism and were present in Bacteroides and Lachnospiraceae. Therefore, they are considered keystone bacteria in xylitol digestion. Also, xylitol affected the metabolic pathway of propionate, significantly promoting the transcription of phosphate acetyltransferase (EC 2.3.1.8) in Bifidobacterium and increasing the production of propionate. Conclusions: Our results revealed that those key enzymes for xylitol digestion from different bacteria can together support the growth of micro-ecology, but they also enhanced the concentration of propionate, which lowered pH to restrict relative amounts of Escherichia and Staphylococcus. Based on the cross-feeding and competition among those bacteria, xylitol can dynamically balance proportions of the gut microbiome to promote enzymes related to xylitol metabolism and SCFAs. CGRfu2_UbvGGd6F7x5LTJk Video Abstract [ABSTRACT FROM AUTHOR]

Sugarcane ethanol fermentation represents a simple microbial community dominated by S. cerevisiae and co-occurring bacteria with a clearly defined functionality. In this study, we dissect the microbial interactions in sugarcane ethanol fermentation by combinatorically reconstituting every possible combination of species, comprising approximately 80% of the biodiversity in terms of relative abundance. Functional landscape analysis shows that higher-order interactions counterbalance the negative effect of pairwise interactions on ethanol yield. In addition, we find that Lactobacillus amylovorus improves the yeast growth rate and ethanol yield by cross-feeding acetaldehyde, as shown by flux balance analysis and laboratory experiments. Our results suggest that Lactobacillus amylovorus could be considered a beneficial bacterium with the potential to improve sugarcane ethanol fermentation yields by almost 3%. These data highlight the biotechnological importance of comprehensively studying microbial communities and could be extended to other microbial systems with relevance to human health and the environment. Industrial sugarcane ethanol fermentations are accomplished by a microbial community dominated by S. cerevisiae and co-occurring bacteria. Here, the authors investigate how microbial community composition contributes to community function and reveal the role of acetaldehyde in improving yeast growth rate and ethanol production. [ABSTRACT FROM AUTHOR]

Summary: Cross‐feeding of metabolites between coexisting cells leads to complex and interconnected elemental cycling and microbial interactions. These relationships influence overall community function and can be altered by changes in substrate availability. Here, we used isotopic rate measurements and metagenomic sequencing to study how cross‐feeding relationships changed in response to stepwise increases of sulfide concentrations in a membrane‐aerated biofilm reactor that was fed with methane and ammonium. Results showed that sulfide: (i) decreased nitrite oxidation rates but increased ammonia oxidation rates; (ii) changed the denitrifying community and increased nitrous oxide production; and (iii) induced dissimilatory nitrite reduction to ammonium (DNRA). We infer that inhibition of nitrite oxidation resulted in higher nitrite availability for DNRA, anammox, and nitrite‐dependent anaerobic methane oxidation. In other words, sulfide likely disrupted microbial cross‐feeding between AOB and NOB and induced cross‐feeding between AOB and nitrite reducing organisms. Furthermore, these cross‐feeding relationships were spatially distributed between biofilm and planktonic phases of the reactor. These results indicate that using sulfide as an electron donor will promote N2O and ammonium production, which is generally not desirable in engineered systems. [ABSTRACT FROM AUTHOR]

Understanding a complex microbial ecosystem such as the human gut microbiome requires information about both microbial species and the metabolites they produce and secrete. These metabolites are exchanged via a large network of cross-feeding interactions, and are crucial for predicting the functional state of the microbiome. However, till date, we only have information for a part of this network, limited by experimental throughput. Here, we propose an ecology-based computational method, GutCP, using which we predict hundreds of new experimentally untested cross-feeding interactions in the human gut microbiome. GutCP utilizes a mechanistic model of the gut microbiome with the explicit exchange of metabolites and their effects on the growth of microbial species. To build GutCP, we combine metagenomic and metabolomic measurements from the gut microbiome with optimization techniques from machine learning. Close to 65% of the cross-feeding interactions predicted by GutCP are supported by evidence from genome annotations, which we provide for experimental testing. Our method has the potential to greatly improve existing models of the human gut microbiome, as well as our ability to predict the metabolic profile of the gut. Understanding a complex microbial ecosystem such as the human gut microbiome requires information about both microbial species and the metabolites they produce and secrete. Here, the authors propose an ecology-based computational method to predict hundreds of new experimentally untested cross-feeding interactions in the human gut microbiome. [ABSTRACT FROM AUTHOR]

Background and Objectives: Pseudomonas aeruginosa is a problematic opportunistic pathogen causing several types of nosocomial infections with a high resistance rate to antibiotics. Production of many virulence factors in P. aeruginosa is regulated by quorum sensing (QS), a cell-to-cell communication mechanism. In this study, we aimed to assess and compare the inhibitory effect of azithromycin (AZM) and EPI-PAβN (efflux pump inhibitor-Phenylalanine-Arginine Beta-Naphthylamide) on QS system and QS-dependent virulence factors in P. aeruginosa clinical isolates. Materials and Methods: A total of 50 P. aeruginosa isolates were obtained from different types of clinical specimens. Isolates were investigated for detection of QS system molecules by AHL cross-feeding bioassay and QS-dependent virulence factors; this was also confirmed by detection of QS genes (lasR, lasI, rhlR, and rhlI) using PCR assay. The inhibitory effect of sub-MIC AZM and EPI PAβN on these virulence factors was assessed. Results: All the P. aeruginosa, producing QS signals C4HSL, failed to produce C4HSL in the presence of sub-MIC AZM, In the presence of EPI PAβN (20 μg/ml) only 14 isolates were affected, there was a significant reduction in QS-dependent virulence factors production (protease, biofilm, rhamnolipid and pyocyanin) in the presence of either 20 μg/ml EPI or sub-MIC of AZM with the inhibitory effect of AZM was more observed than PAβN. Conclusion: Anti-QS agents like AZM and EPI (PAβN) are useful therapeutic options for P. aeruginosa due to its inhibitory effect on QS-dependent virulence factors production without selective pressure on bacteria growth, so resistance to these agents is less likely to develop. [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]

The fundamental niches of bacteria can be defined along many environmental axes, including temperature tolerance and resources consumed, while interactions with other organisms can constrain (e.g. competition) or enlarge (e.g. cross-feeding) realized niches. Organisms are often categorized as generalists or specialists, corresponding to broad or narrow niche requirements, which can then be linked to their functional role in an ecosystem. We show how these terms are applied to bacteria, make predictions about how the type and extent of generalism displayed by an organism relates to its functional potential and discuss the value of collecting different types of generalist bacteria. We believe that new approaches that take advantage of both high-throughput sequencing and environmental manipulation can allow us to understand the many types of generalism found within both cultivated and yet-to-be-cultivated bacteria. [ABSTRACT FROM AUTHOR]

The evolution of cross-feeding among individuals of the same species can help generate genetic and phenotypic diversity even in completely homogeneous environments. Cross-feeding Escherichia coli strains, where one strain feeds on a carbon source excreted by another strain, rapidly emerge during experimental evolution in a chemically minimal environment containing glucose as the sole carbon source. Genome-scale metabolic modeling predicts that cross-feeding of 58 carbon sources can emerge in the same environment, but only cross-feeding of acetate and glycerol has been experimentally observed. Here we use metabolic modeling to ask whether acetate and glycerol cross-feeding are especially likely to evolve, perhaps because they require less metabolic change, and thus perhaps also less genetic change than other cross-feeding interactions. However, this is not the case. The minimally required metabolic changes required for acetate and glycerol cross feeding affect dozens of chemical reactions, multiple biochemical pathways, as well as multiple operons or regulons. The complexity of these changes is consistent with experimental observations, where cross-feeding strains harbor multiple mutations. The required metabolic changes are also no less complex than those observed for multiple other of the 56 cross feeding interactions we study. We discuss possible reasons why only two cross-feeding interactions have been discovered during experimental evolution and argue that multiple new cross-feeding interactions may await discovery. Author summary: The evolution of cross-feeding interactions, where one organism thrives by consuming the excretions of others, can create diversity even in simple and homogeneous environments. In past work, we had predicted that 58 cross-feeding interactions could evolve in populations of E. coli grown in glucose minimal media, yet only two have been experimentally observed, those involving acetate and glycerol. We hypothesized that multiple mutations might be required for the evolution of computationally predicted but not experimentally observed cross-feeding interactions. To answer this question, we developed a method that searches for the minimal number of metabolic changes required for individuals to change their metabolic state (from an ancestral glucose-consuming state to an evolved state that produces or consumes other metabolite). We observed that the metabolic changes required for the evolution of acetate and glycerol cross-feeding are no less complex than those required for the evolution of the other predicted cross-feeding interactions, which suggests that multiple cross-feeding interactions may still await discovery. [ABSTRACT FROM AUTHOR]

Dissolved organic nitrogen (DON) compounds such as methylamines (MAs) and glycine betaine (GBT) occur at detectable concentrations in marine habitats and are also produced and released by microalgae. For many marine bacteria, these DON compounds can serve as carbon, energy, and nitrogen sources, but microalgae usually cannot metabolize them. Interestingly though, it was previously shown that Donghicola sp. strain KarMa—a member of the marine Rhodobacteraceae —can cross-feed ammonium such that the ammonium it produces upon degrading monomethylamine (MMA) then serves as nitrogen source for the diatom Phaeodactylum tricornutum ; thus, these organisms form a mutual metabolic interaction under photoautotrophic conditions. In the present study, we investigated whether this interaction plays a broader role in bacteria–diatom interactions in general. Results showed that cross-feeding between strain KarMa and P. tricornutum was also possible with di- and trimethylamine as well as with GBT. Further, cross-feeding of strain KarMa was also observed in cocultures with the diatoms Amphora coffeaeformis and Thalassiosira pseudonana with MMA as the sole nitrogen source. Regarding cross-feeding involving other Rhodobacteraceae strains, the in silico analysis of MA and GBT degradation pathways indicated that algae-associated Rhodobacteraceae -type strains likely interact with P. tricornutum in a similar manner as the strain KarMa does. For these types of strains (such as Celeribacter halophilus , Roseobacter denitrificans , Roseovarius indicus , Ruegeria pomeroyi , and Sulfitobacter noctilucicola), ammonium cross-feeding after methylamine degradation showed species-specific patterns, whereas bacterial GBT degradation always led to diatom growth. Overall, the degradation of DON compounds by the Rhodobacteraceae family and the subsequent cross-feeding of ammonium may represent a widespread, organism-specific, and regulated metabolic interaction for establishing and stabilizing associations with photoautotrophic diatoms in the oceans. [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]

Women with bacterial vaginosis (BV), an imbalance of the vaginal microbiome, are more likely to be colonized by potential pathogens such as Fusobacterium nucleatum, a bacterium linked with intrauterine infection and preterm birth. However, the conditions and mechanisms supporting pathogen colonization during vaginal dysbiosis remain obscure. We demonstrate that sialidase activity, a diagnostic feature of BV, promoted F. nucleatum foraging and growth on mammalian sialoglycans, a nutrient resource that was otherwise inaccessible because of the lack of endogenous F. nucleatum sialidase. In mice with sialidase-producing vaginal microbiotas, mutant F. nucleatum unable to consume sialic acids was impaired in vaginal colonization. These experiments in mice also led to the discovery that F. nucleatum may also "give back" to the community by reinforcing sialidase activity, a biochemical feature of human dysbiosis. Using human vaginal bacterial communities, we show that F. nucleatum supported robust outgrowth of Gardnerella vaginalis, a major sialidase producer and one of the most abundant organisms in BV. These results illustrate that mutually beneficial relationships between vaginal bacteria support pathogen colonization and may help maintain features of dysbiosis. These findings challenge the simplistic dogma that the mere absence of "healthy" lactobacilli is the sole mechanism that creates a permissive environment for pathogens during vaginal dysbiosis. Given the ubiquity of F. nucleatum in the human mouth, these studies also suggest a possible mechanism underlying links between vaginal dysbiosis and oral sex. Bacterial mutualism involving the prominent oral bacterium Fusobacterium nucleatum may drive vaginal dysbiosis in women and could help to explain the clinical correlations between vaginal dysbiosis and oral sex. [ABSTRACT FROM AUTHOR]

Social interaction between microbes can be described at many levels of details: from the biochemistry of cell-cell interactions to the ecological dynamics of populations. Choosing an appropriate level to model microbial communities without losing generality remains a challenge. Here we show that modeling cross-feeding interactions at an intermediate level between genome-scale metabolic models of individual species and consumer-resource models of ecosystems is suitable to experimental data. We applied our modeling framework to three published examples of multi-strain Escherichia coli communities with increasing complexity: uni-, bi-, and multi-directional cross-feeding of either substitutable metabolic byproducts or essential nutrients. The intermediate-scale model accurately fit empirical data and quantified metabolic exchange rates that are hard to measure experimentally, even for a complex community of 14 amino acid auxotrophies. By studying the conditions of species coexistence, the ecological outcomes of cross-feeding interactions, and each community's robustness to perturbations, we extracted new quantitative insights from these three published experimental datasets. Our analysis provides a foundation to quantify cross-feeding interactions from experimental data, and highlights the importance of metabolic exchanges in the dynamics and stability of microbial communities. Author summary: The behavior of microbial communities such as the human microbiome is hard to predict by its species composition alone. Our efforts to engineer microbiomes—for example to improve human health—would benefit from mathematical models that accurately describe how microbes exchange metabolites with each other and how their environment shapes these exchanges. But what is an appropriate level of details for those models? We propose an intermediate level to model metabolic exchanges between microbes. We show that these models can accurately describe population dynamics in three laboratory communities and predicts their stability in response to perturbations such as changes in the nutrients available in the medium that they grow on. Our work suggests that a highly detailed metabolic network model is unnecessary for extracting ecological insights from experimental data and improves mathematical models so that one day we may be able to predict the behavior of real-world communities such as the human microbiome. [ABSTRACT FROM AUTHOR]

With antibiotic resistance rates on the rise, it is critical to understand how microbial species interactions influence the evolution of resistance. In obligate mutualisms, the survival of any one species (regardless of its intrinsic resistance) is contingent on the resistance of its cross-feeding partners. This sets the community antibiotic sensitivity at that of the 'weakest link' species. In this study, we tested the hypothesis that weakest link dynamics in an obligate cross-feeding relationship would limit the extent and mechanisms of antibiotic resistance evolution. We experimentally evolved an obligate co-culture and monoculture controls along gradients of two different antibiotics. We measured the rate at which each treatment increased antibiotic resistance, and sequenced terminal populations to question whether mutations differed between mono- and co-cultures. In both rifampicin and ampicillin treatments, we observed that resistance evolved more slowly in obligate co-cultures of E. coli and S. enterica than in monocultures. While we observed similar mechanisms of resistance arising under rifampicin selection, under ampicillin selection different resistance mechanisms arose in co-cultures and monocultures. In particular, mutations in an essential cell division protein, ftsI, arose in S. enterica only in co-culture. A simple mathematical model demonstrated that reliance on a partner is sufficient to slow the rate of adaptation, and can change the distribution of adaptive mutations that are acquired. Our results demonstrate that cooperative metabolic interactions can be an important modulator of resistance evolution in microbial communities. Author summary: Little is known about how ecological interactions between bacteria influence the evolution of antibiotic resistance. We tested the impact of metabolic interactions on resistance evolution in an engineered two-species bacterial community. Through experimental and modeling work, we found that obligate metabolic interdependency slows the rate of resistance acquisition, and can change the type and magnitude of resistance mutations that evolve. This work suggests that resistance evolution may be slowed by targeting both a pathogen and its metabolic partners with antibiotics. Additionally, we showed that community context can generate novel trajectories through which antibiotic resistance evolves. [ABSTRACT FROM AUTHOR]

Microbial interactions abound in natural ecosystems and shape community structure and function. Substantial attention has been given to cataloging mechanisms by which microbes interact, but there is a limited understanding of the genetic landscapes that promote or hinder microbial interactions. We previously developed a mutualistic coculture pairing Escherichia coli and Rhodopseudomonas palustris, wherein E. coli provides carbon to R. palustris in the form of glucose fermentation products and R. palustris fixes N2 gas and provides nitrogen to E. coli in the form of NH4 +31. The stable coexistence and reproducible trends exhibited by this coculture make it ideal for interrogating the genetic underpinnings of a cross-feeding mutualism. Here, we used random barcode transposon sequencing (RB-TnSeq) to conduct a genome-wide search for E. coli genes that influence fitness during cooperative growth with R. palustris. RB-TnSeq revealed hundreds of genes that increased or decreased E. coli fitness in a mutualism dependent manner. Some identified genes were involved in nitrogen sensing and assimilation, as expected given the coculture design. The other identified genes were involved in diverse cellular processes, including energy production and cell wall and membrane biogenesis. Additionally, we discovered unexpected purine cross-feeding from R. palustris to E. coli, with coculture rescuing growth of an E. coli purine auxotroph. Our data provide insight into the genes and gene networks that can influence a cross-feeding mutualism and underscore that microbial interactions are not necessarily predictable a priori. [ABSTRACT FROM AUTHOR]

Cross-feeding based on the metabolite 1,2-propanediol has been proposed to have an important role in the establishment of trophic interactions among gut symbionts, but its ecological importance has not been empirically established. Here, we show that in vitro growth of Lactobacillus reuteri (syn. Limosilactobacillus reuteri) ATCC PTA 6475 is enhanced through 1,2-propanediol produced by Bifidobacterium breve UCC2003 and Escherichia coli MG1655 from the metabolization of fucose and rhamnose, respectively. Work with isogenic mutants showed that the trophic interaction is dependent on the pduCDE operon in L. reuteri, which encodes the ability to use 1,2-propanediol, and the L-fucose permease (fucP) gene in B. breve, which is required for 1,2-propanediol formation from fucose. Experiments in gnotobiotic mice revealed that, although the pduCDE operon bestows a fitness burden on L. reuteri ATCC PTA 6475 in the mouse digestive tract, the ecological performance of the strain was enhanced in the presence of B. breve UCC2003 and the mucus-degrading species Bifidobacterium bifidum. The use of the respective pduCDE and fucP mutants of L. reuteri and B. breve in the mouse experiments indicated that the trophic interaction was specifically based on 1,2-propanediol. Overall, our work established the ecological importance of cross-feeding relationships based on 1,2-propanediol for the fitness of a bacterial symbiont in the vertebrate gut. IMPORTANCE Through experiments in gnotobiotic mice that employed isogenic mutants of bacterial strains that produce (Bifidobacterium breve) and utilize (Lactobacillus reuteri) 1,2-propanediol, this study provides mechanistic insight into the ecological ramifications of a trophic interaction between gut symbionts. The findings improve our understanding on how cross-feeding influences the competitive fitness of L. reuteri in the vertebrate gut and revealed a putative selective force that shaped the evolution of the species. The findings are relevant since they provide a basis to design rational microbialbased strategies to modulate gut ecosystems, which could employ mixtures of bacterial strains that establish trophic interactions or a personalized approach based on the ability of a resident microbiota to provide resources for the incoming microbe. [ABSTRACT FROM AUTHOR]

Thestrengthofbioticinteractions withinanecological communityaffectsthe susceptibility of the community to invasion by introduced taxa. In microbial communities, cross-feeding is a widespread type of biotic interaction that has the potential to affect community assembly and stability. Yet, there is little understanding of how the presence of cross-feeding within a community affects invasion risk. Here, I develop a metabolite-explicit model where native microbial taxa interact through both cross-feeding and competition for metabolites. I use this model to study how the strength of biotic interactions, especially cross-feeding, influence whether an introduced taxon can join the community. I found that stronger cross-feeding and competition led to much lower invasion risk, as both types of biotic interactions lead to greater metabolite scarcity for the invader. I also evaluated the impact of a successful invader on community composition and structure. The effect of invaders on the native community was greatest at intermediate levels of cross-feeding; at this ‘critical’ level of cross-feeding, successful invaders generally cause decreased diversity, decreased productivity, greater metabolite availability, and decreased quantities of metabolites exchanged among taxa. Furthermore, these changes resulting from a successful primary invader made communities further susceptible to future invaders. The increase in invasion risk was greatest when the network of metabolite exchange between taxa was minimally redundant. Thus, this model demonstrates a case of invasional meltdown that is mediated by initial invaders disrupting the metabolite exchange networks of the native community. [ABSTRACT FROM AUTHOR]

The spatial organization of microbial communities arises from a complex interplay of biotic and abiotic interactions, and is a major determinant of ecosystem functions. Here we design a microfluidic platform to investigate how the spatial arrangement of microbes impacts gene expression and growth. We elucidate key biochemical parameters that dictate the mapping between spatial positioning and gene expression patterns. We show that distance can establish a low-pass filter to periodic inputs and can enhance the fidelity of information processing. Positive and negative feedback can play disparate roles in the synchronization and robustness of a genetic oscillator distributed between two strains to spatial separation. Quantification of growth and metabolite release in an amino-acid auxotroph community demonstrates that the interaction network and stability of the community are highly sensitive to temporal perturbations and spatial arrangements. In sum, our microfluidic platform can quantify spatiotemporal parameters influencing diffusion-mediated interactions in microbial consortia. The spatial organisation of microbial communities is caused by the interplay of biotic and abiotic factors. Here the authors design a microfluidic platform to quantify the spatiotemporal parameters influencing diffusion-mediated interactions, and use this device to investigate information transmission and metabolic cross-feeding in synthetic microbial consortia. [ABSTRACT FROM AUTHOR]

All microorganisms release many metabolites, collectively known as the exometabolome. The resultant multi-way cross-feeding of metabolites among microorganisms distributes resources, thereby increasing total biomass of the microbial community, and promotes the recruitment and persistence of phylogenetically and functionally diverse taxa in microbial communities. Metabolite transfer can also select for evolutionary diversification, yielding multiple closely related but functionally distinct strains. Depending on starting conditions, the evolved strains may be auxotrophs requiring metabolic outputs from producer cells or, alternatively, display loss of complementary reactions in metabolic pathways, with increased metabolic efficiency. Metabolite cross-feeding is widespread in many microbial communities associated with animals and plants, including the animal gut microbiome, and these metabolic interactions can yield products valuable to the host. However, metabolite exchange between pairs of intracellular microbial taxa that share the same host cell or organ can be very limited compared to pairs of free-living microorganisms, perhaps as a consequence of host controls over the metabolic function of intracellular microorganisms. Priorities for future research include the development of tools for improved quantification of metabolite exchange in complex communities and greater integration of the roles of metabolic cross-feeding and other ecological processes, including priority effects and antagonistic interactions, in shaping microbial communities. [ABSTRACT FROM AUTHOR]

In microbial ecosystems, species not only compete for common resources but may also display mutualistic interactions as a result from metabolic cross-feeding. Such mutualism can lead to bistability. Depending on the initial population sizes, species will either survive or go extinct. Various phenomenological models have been suggested to describe bistability in mutualistic systems. However, these models do not account for interaction mediators such as nutrients. In contrast, nutrient-explicit models do not provide an intuitive understanding of what causes bistability. Here, we reduce a theoretical nutrient-explicit model of two mutualistic cross-feeders in a chemostat, uncovering an explicit relation to a growth model with an Allee effect. We show that the dilution rate in the chemostat leads to bistability by turning a weak Allee effect into a strong Allee effect. This happens as long as there is more production than consumption of cross-fed nutrients. Thanks to the explicit relationship of the reduced model with the underlying experimental parameters, these results allow to predict the biological conditions that sustain or prevent the survival of mutualistic species. [ABSTRACT FROM AUTHOR]

There is the notion that infection with a virulent intestinal pathogen induces generally stronger mucosal adaptive immunity than the exposure to an avirulent strain. Whether the associated mucosal inflammation is important or redundant for effective induction of immunity is, however, still unclear. Here we use a model of auxotrophic Salmonella infection in germ-free mice to show that live bacterial virulence factor-driven immunogenicity can be uncoupled from inflammatory pathogenicity. Although live auxotrophic Salmonella no longer causes inflammation, its mucosal virulence factors remain the main drivers of protective mucosal immunity; virulence factor-deficient, like killed, bacteria show reduced efficacy. Assessing the involvement of innate pathogen sensing mechanisms, we show MYD88/TRIF, Caspase-1/Caspase-11 inflammasome, and NOD1/NOD2 nodosome signaling to be individually redundant. In colonized animals we show that microbiota metabolite cross-feeding may recover intestinal luminal colonization but not pathogenicity. Consequent immunoglobulin A immunity and microbial niche competition synergistically protect against Salmonella wild-type infection. Virulent pathogens generally induce a stronger mucosal immunity than avirulent strains, but whether the associated inflammation is necessary for this is unclear. Here, using auxotrophic Salmonella enterica, the authors show that virulence factor function determines induction of protective IgA. [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]

Anaerobic digestion of municipal and other organic waste is a microbial process for conversion of complex organic substances to biogas (a renewable energy source) comprising a mixture of methane and CO2, and a stabilized sludge, which may be used as an organic fertilizer. Diverse groups of the methanogenic microbial community degrade complex organic compounds into simple fermentation products such as hydrogen, formate, acetate, short-chained volatile fatty acids, ethanol, etc. These low-molecular mass products act as the substrates and carriers involved in biogas production by syntrophic bacteria and methanogenic archaea at the methanogenesis stage, the last stage of the anaerobic process. The present review discusses syntrophic interactions between the microorganisms involved in anaerobic degradation of organic substances, as well as two types of interspecies electron transfer (IET): indirect IET (IIET, Indirect Interspecies Electron Transfer) and direct IET (DIET, Direct Interspecies Electron Transfer). DIET-based syntrophic interactions between microorganisms may be stimulated by adding conductive materials into anaerobic digesters, which may have the potential for practical applications. [ABSTRACT FROM AUTHOR]

Summary: It has been recently shown that magnetite nanoparticles (nanoFe3O4) can facilitate methanogenic syntrophy but the effect of magnetite on methanogenesis alone remains elusive. Here we show that aceticlastic methanogenesis by Methanosarcina mazei is accelerated by magnetite and is correlated with the redox cycling of structural Fe(II) and Fe(III) in the mineral. An enrichment and its closest pure culture relative, Ms. mazei zm‐15, both obtained from a natural wetland of the Tibetan plateau were tested in this experiment. The Fe(II) to Fe(III) ratios in magnetite, as measured by multiple approaches, show an initial increase in both the methanogenic cultures and the blank preparations containing no microbes. The Fe(II)/Fe(III) ratio then displays a distinct decline followed by an increase towards the end of incubation only in the enrichment and pure culture cultivations. This redox cycling of magnetite is in accordance with the stimulation of aceticlastic methanogenesis. Microscopic observation reveals the precipitation of nanoFe3O4 on methanogen cell surface. The genomic analysis predicts that in addition to electron transfer components essential for aceticlastic methanogenesis, Ms. mazei zm‐15 contains an outer‐surface multiheme c‐type cytochrome (MHC) and a few function‐unknown surface proteins that harbour monoheme motif. We hypothesize that the redox cycling of nanoFe3O4 delivers a positive influence via the MHC to the membrane electron transfer chain and hence promote the aceticlastic methanogenesis. [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]

Vitamin B12 (VB12) is a critical micronutrient that controls DNA metabolic pathways to maintain the host genomic stability and tissue homeostasis. We recently reported that the newly discovered commensal Propionibacterium, P. UF1, regulates the intestinal immunity to resist pathogen infection, which may be attributed in part to VB12 produced by this bacterium. Here we demonstrate that VB12 synthesized by P. UF1 is highly dependent on cobA gene-encoding uroporphyrinogen III methyltransferase, and that this vitamin distinctively regulates the cobA operon through its 5' untranslated region (5' UTR). Furthermore, conserved secondary structure and mutagenesis analyses revealed a VB12-riboswitch, cbiMCbl (140 bp), within the 5' UTR that controls the expression of downstream genes. Intriguingly, ablation of the cbiMCbl significantly dysregulates the biosynthesis of VB12, illuminating the significance of this riboswitch for bacterial VB12 biosynthesis. Collectively, our finding is an in-depth report underscoring the regulation of VB12 within the beneficial P. UF1 bacterium, through which the commensal metabolic network may improve gut bacterial cross-feeding and human health. [ABSTRACT FROM AUTHOR]