Some are more equal than others: the role of "keystone" species in the degradation of recalcitrant substrates

Utilization of diverse probiotics to create human health promoting fatty acids: A review

Many probiotics produce functional lipids with health-promoting properties, such as short-chain fatty acids, linoleic acid and omega-3 fatty acids. They have been shown to maintain gut health, strengthen the intestinal barrier, and have anti-inflammatory and antioxidant effects. In this article, we provide an up-to-date review of the various functional lipids produced by probiotics. These probiotics can be incorporated into foods, supplements, or pharmaceuticals to produce these functional lipids in the human colon, or they can be used in industrial biotechnology processes to generate functional lipids, which are then isolated and used as ingredients. We then highlight the different physiological functions for which they may be beneficial to human health, in addition to discussing some of the challenges of incorporating probiotics into commercial products and some potential solutions to address these challenges. Finally, we highlight the importance of testing the efficacy and safety of the new generation of probiotic-enhanced products, as well as the great potential for the marketization of related products.

The ruminant gut microbiome vs enteric methane emission: The essential microbes may help to mitigate the global methane crisis

Ruminants release enteric methane into the atmosphere, significantly increasing greenhouse gas emissions and degrading the environment. A common focus of traditional mitigation efforts is on dietary management and manipulation, which may have limits in sustainability and efficacy, exploring the potential of essential microorganisms as a novel way to reduce intestinal methane emissions in ruminants; a topic that has garnered increased attention in recent years. Fermentation and feed digestion are significantly aided by essential microbes found in the rumen, such as bacteria, fungi, and archaea. The practical implications of the findings reported in various studies conducted on rumen gut concerning methane emissions may pave the way to understanding the mechanisms of CH4 production in the rumen to enhance cattle feed efficiency and mitigate CH4 emissions from livestock. This review discussed using essential bacteria to reduce intestinal methane emissions in ruminants. It investigates how particular microbial strains or consortia can alter rumen fermentation pathways to lower methane output while preserving the health and productivity of animals. We also describe the role of probiotics and prebiotics in managing methane emissions using microbial feed additives. Further, recent studies involving microbial interventions have been discussed. The use of new methods involving functional metagenomics and meta-transcriptomics for exploring the rumen microbiome structure has been highlighted. This review also emphasizes the challenges faced in altering the gut microbiome and future directions in this area.

The pectin metabolizing capacity of the human gut microbiota

The human gastrointestinal microbiota, densely populated with a diverse array of microorganisms primarily from the bacterial phyla Bacteroidota, Bacillota, and Actinomycetota, is crucial for maintaining health and physiological functions. Dietary fibers, particularly pectin, significantly influence the composition and metabolic activity of the gut microbiome. Pectin is fermented by gut bacteria using carbohydrate-active enzymes (CAZymes), resulting in the production of short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate, which provide various health benefits. The gastrointestinal microbiota has evolved to produce CAZymes that target different pectin components, facilitating cross-feeding within the microbial community. This review explores the fermentation of pectin by various gut bacteria, focusing on the involved transport systems, CAZyme families, SCFA synthesis capacity, and effects on microbial ecology in the gut. It addresses the complexities of the gut microbiome's response to pectin and highlights the importance of microbial cross-feeding in maintaining a balanced and diverse gut ecosystem. Through a systematic analysis of pectinolytic CAZyme production, this review provides insights into the enzymatic mechanisms underlying pectin degradation and their broader implications for human health, paving the way for more targeted and personalized dietary strategies.

Purified fibers in chemically defined synthetic diets destabilize the gut microbiome of an omnivorous insect model

The macronutrient composition of a host's diet shapes its gut microbial community, with dietary fiber in particular escaping host digestion to serve as a potent carbon source for gut microbiota. Despite widespread recognition of fiber's importance to microbiome health, nutritional research often fails to differentiate hyper-processed fibers from cell-matrix derived intrinsic fibers, limiting our understanding of how individual polysaccharides influence the gut community. We use the American cockroach (Periplaneta americana) as a model system to dissect the response of complex gut microbial communities to diet modifications that are impossible to test in traditional host models. Here, we designed synthetic diets from lab-grade, purified ingredients to identify how the cockroach microbiome responds to six different carbohydrates (chitin, methylcellulose, microcrystalline cellulose, pectin, starch, xylan) in otherwise balanced diets. We show via 16S rRNA gene profiling that these synthetic diets reduce bacterial diversity and alter the phylogenetic composition of cockroach gut microbiota in a fiber-dependent manner, regardless of the vitamin and protein content of the diet. Comparisons with cockroaches fed whole-food diets reveal that synthetic diets induce blooms in common cockroach-associated taxa and subsequently fragment previously stable microbial correlation networks. Our research leverages an unconventional microbiome model system and customizable lab-grade artificial diets to shed light on how purified polysaccharides, as opposed to nutritionally complex intrinsic fibers, exert substantial influence over a normally stable gut community.

From Food Waste to Sustainable Agriculture: Nutritive Value of Potato By-Product in Total Mixed Ration for Angus Bulls

Raw potato fries are a type of potato by-product (PBP), and they have great potential as a partial replacement of grain in animal feeds to improve the environmental sustainability of food production. This study aimed to investigate the effects of replacing corn with different levels of PBP (0%, 12.84%, 25.65%, and 38.44%) in the total mixed ration (TMR) of Angus bull. Sixty 16-month-old Angus bulls (548.5 ± 15.0 kg, mean ± SD) were randomly assigned to four treatments. The results indicated that with the increase in the substitution amount of PBP, the body weight decreased significantly. The dry matter apparent digestibility and starch apparent digestibility linearly decreased as PBP replacement increased. The feed ingredient composition in the TMR varied, leading to a corresponding change in the rumen microbiota, especially in cellulolytic bacteria and amylolytic bacteria. The abundance of Succiniclasticum in the 12.84% PBP and 38.44% PBP diets was significantly higher than that in the 0% PBP and 25.65% PBP diets. The abundance of Ruminococcus linearly increased. In conclusion, using PBP to replace corn for beef cattle had no negative impact on rumen fermentation, and the decrease in apparent digestibility explained the change in growth performance. Its application in practical production is highly cost-effective and a strategy to reduce food waste.

Fibrobacter sp. HC4, a newly isolated strain, demonstrates a high cellulolytic activity as revealed by enzymatic measurements and in vitro assay

Despite their low quantity and abundance, the cellulolytic bacteria that inhabit the equine large intestine are vital to their host, as they enable the crucial use of forage-based diets. Fibrobacter succinogenes is one of the most important intestinal cellulolytic bacteria. In this study, Fibrobacter sp. HC4, one cellulolytic strain newly isolated from the horse cecum, was characterized for its ability to utilize plant cell wall fibers. Fibrobacter sp. HC4 consumed only cellulose, cellobiose, and glucose and produced succinate and acetate in equal amounts. Among genes coding for CAZymes, 26% of the detected glycoside hydrolases (GHs) were involved in cellulolysis. These cellulases belong to the GH5, GH8, GH9, GH44, GH45, and GH51 families. Both carboxymethyl cellulase and xylanase activities of Fibrobacter sp. HC4 were detected using the Congo red method and were higher than those of F. succinogenes S85, the type strain. The in vitro addition of Fibrobacter sp. HC4 to a fecal microbial ecosystem of horses with large intestinal acidosis significantly enhanced fibrolytic activity as measured by the increase in gas and volatile fatty acids production during the first 48 h. According to this, the pH decreased and the disappearance of dry matter increased at a faster rate with Fibrobacter sp. HC4. Our data suggest a high specialization of the new strain in cellulose degradation. Such a strain could be of interest for future exploitation of its probiotic potential, which needs to be further determined by in vivo studies.IMPORTANCECellulose is the most abundant of plant cell wall fiber and can only be degraded by the large intestine microbiota, resulting in the production of volatile fatty acids that are essential for the host nutrition and health. Consequently, cellulolytic bacteria are of major importance to herbivores. However, these bacteria are challenged by various factors, such as high starch diets, which acidify the ecosystem and reduce their numbers and activity. This can lead to an imbalance in the gut microbiota and digestive problems such as colic, a major cause of mortality in horses. In this work, we characterized a newly isolated cellulolytic strain, Fibrobacter sp. HC4, from the equine intestinal microbiota. Due to its high cellulolytic capacity, reintroduction of this strain into an equine fecal ecosystem stimulates hay fermentation in vitro. Isolating and describing cellulolytic bacteria is a prerequisite for using them as probiotics to restore intestinal balance.

Ruminococcus torques is a keystone degrader of intestinal mucin glycoprotein, releasing oligosaccharides used by Bacteroides thetaiotaomicron

Symbiotic interactions between humans and our communities of resident gut microbes (microbiota) play many roles in health and disease. Some gut bacteria utilize mucus as a nutrient source and can under certain conditions damage the protective barrier it forms, increasing disease susceptibility. We investigated how Ruminococcus torques-a known mucin degrader that has been implicated in inflammatory bowel diseases (IBDs)-degrades mucin glycoproteins or their component O-linked glycans to understand its effects on the availability of mucin-derived nutrients for other bacteria. We found that R. torques utilizes both mucin glycoproteins and released oligosaccharides from gastric and colonic mucins, degrading these substrates with a panoply of mostly constitutively expressed, secreted enzymes. Investigation of mucin oligosaccharide degradation by R. torques revealed strong α-L-fucosidase, sialidase and β1,4-galactosidase activities. There was a lack of detectable sulfatase and weak β1,3-galactosidase degradation, resulting in accumulation of glycans containing these structures on mucin polypeptides. While the Gram-negative symbiont, Bacteroides thetaiotaomicron grows poorly on mucin glycoproteins, we demonstrate a clear ability of R. torques to liberate products from mucins, making them accessible to B. thetaiotaomicron. This work underscores the diversity of mucin-degrading mechanisms in different bacterial species and the probability that some species are contingent on others for the ability to more fully access mucin-derived nutrients. The ability of R. torques to directly degrade a variety of mucin and mucin glycan structures and unlock released glycans for other species suggests that it is a keystone mucin degrader, which might contribute to its association with IBD.IMPORTANCEAn important facet of maintaining healthy symbiosis between host and intestinal microbes is the mucus layer, the first defense protecting the epithelium from lumenal bacteria. Some gut bacteria degrade the various components of intestinal mucins, but detailed mechanisms used by different species are still emerging. It is imperative to understand these mechanisms as they likely dictate interspecies interactions and may illuminate species associated with bacterial mucus damage and subsequent disease susceptibility. Ruminococcus torques is positively associated with IBD in multiple studies. We identified mucin glycan-degrading enzymes in R. torques and found that it shares mucin degradation products with another species of gut bacteria, Bacteroides thetaiotaomicron. Our findings underscore the importance of understanding mucin degradation mechanisms in different gut bacteria and their consequences on interspecies interactions, which may identify keystone bacteria that disproportionately affect mucus damage and could therefore be key players in effects that result from reductions in mucus integrity.

The mechanisms in the gut microbiota regulation and type 2 diabetes therapeutic activity of resistant starches

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.

Designing function-specific minimal microbiomes from large microbial communities

Microorganisms exist in large communities of diverse species, exhibiting various functionalities. The mammalian gut microbiome, for instance, has the functionality of digesting dietary fibre and producing different short-chain fatty acids. Not all microbes present in a community contribute to a given functionality; it is possible to find a minimal microbiome, which is a subset of the large microbiome, that is capable of performing the functionality while maintaining other community properties such as growth rate and metabolite production. Such a minimal microbiome will also contain keystone species for SCFA production in that community. In this work, we present a systematic constraint-based approach to identify a minimal microbiome from a large community for a user-proposed function. We employ a top-down approach with sequential deletion followed by solving a mixed-integer linear programming problem with the objective of minimising the L1-norm of the membership vector. Notably, we consider quantitative measures of community growth rate and metabolite production rates. We demonstrate the utility of our algorithm by identifying the minimal microbiomes corresponding to three model communities of the gut, and discuss their validity based on the presence of the keystone species in the community. Our approach is generic, flexible and finds application in studying a variety of microbial communities. The algorithm is available from https://github.com/RamanLab/minMicrobiome .

Viral community distribution, assembly mechanism, and associated hosts in an industrial park wastewater treatment plant

Viruses manipulate bacterial community composition and impact wastewater treatment efficiency. Some viruses pose threats to the environment and human populations through infection. Improving the efficiency of wastewater treatment and ensuring the health of the effluent and receptor pools requires an understanding of how viral communities assemble and interact with hosts in wastewater treatment plants (WWTPs). We used metagenomic analysis to study the distribution, assembly mechanism, and sensitive hosts for the viral communities in raw water, anaerobic tanks, and returned activated sludge units of a large-scale industrial park WWTP. Uroviricota (53.42% ± 0.14%) and Nucleocytoviricota (26.1% ± 0.19%) were dominant in all units. Viral community composition significantly differed between units, as measured by β diversity (P = 0.005). Compared to raw water, the relative viral abundance decreased by 29.8% in the anaerobic tank but increased by 9.9% in the activated sludge. Viral community assembly in raw water and anaerobic tanks was predominantly driven by deterministic processes (MST <0.5) versus stochastic processes (MST >0.5) in the activated sludge, indicating that differences in diffusion limits may fundamentally alter the assembly mechanisms of viral communities between the solid and liquid-phase environments. Acidobacteria was identified as the sensitive host contributing to viral abundance, exhibiting strong interactions and a mutual dependence (degree = 59). These results demonstrate the occurrence and prevalence of viruses in WWTPs, their different assembly mechanism, and sensitive hosts. These observations require further study of the mechanisms of viral community succession, ecological function, and roles in the successive wastewater treatment units.

Current Understanding of Equine Gut Dysbiosis and Microbiota Manipulation Techniques: Comparison with Current Knowledge in Other Species

Understanding the importance of intestinal microbiota in horses and the factors influencing its composition have been the focus of many studies over the past few years. Factors such as age, diet, antibiotic administration, and geographic location can affect the gut microbiota. The intra- and inter-individual variability of fecal microbiota in horses complicates its interpretation and has hindered the establishment of a clear definition for dysbiosis. Although a definitive causal relationship between gut dysbiosis in horses and diseases has not been clearly identified, recent research suggests that dysbiosis may play a role in the pathogenesis of various conditions, such as colitis and asthma. Prebiotics, probiotics, and fecal microbiota transplantation to modulate the horse's gastrointestinal tract may eventually be considered a valuable tool for preventing or treating diseases, such as antibiotic-induced colitis. This article aims to summarize the current knowledge on the importance of intestinal microbiota in horses and factors influencing its composition, and also to review the published literature on methods for detecting dysbiosis while discussing the efficacy of gut microbiota manipulation in horses.

Exploring the hemicellulolytic properties and safety of Bacillus paralicheniformis as stepping stone in the use of new fibrolytic beneficial microbes

Bacillus strains from the Moroccan Coordinated Collections of Microorganisms (CCMM) were characterised and tested for fibrolytic function and safety properties that would be beneficial for maintaining intestinal homeostasis, and recommend beneficial microbes in the field of health promotion research. Forty strains were investigated for their fibrolytic activities towards complex purified polysaccharides and natural fibres representative of dietary fibres (DFs) entering the colon for digestion. We demonstrated hemicellulolytic activities for nine strains of Bacillus aerius, re-identified as Bacillus paralicheniformis and Bacillus licheniformis, using xylan, xyloglucan or lichenan as purified polysaccharides, and orange, apple and carrot natural fibres, with strain- and substrate-dependent production of glycoside hydrolases (GHs). Our combined methods, based on enzymatic assays, secretome, and genome analyses, highlighted the hemicellulolytic activities of B. paralicheniformis and the secretion of specific glycoside hydrolases, in particular xylanases, compared to B. licheniformis. Genomic features of these strains revealed a complete set of GH genes dedicated to the degradation of various polysaccharides from DFs, including cellulose, hemicellulose and pectin, which may confer on the strains the ability to digest a variety of DFs. Preliminary experiments on the safety and immunomodulatory properties of B. paralicheniformis fibrolytic strains were evaluated in light of applications as beneficial microbes' candidates for health improvement. B. paralicheniformis CCMM B969 was therefore proposed as a new fibrolytic beneficial microbe candidate.

Methionine restriction-induced sulfur deficiency impairs antitumour immunity partially through gut microbiota

Restriction of methionine (MR), a sulfur-containing essential amino acid, has been reported to repress cancer growth and improve therapeutic responses in several preclinical settings. However, how MR impacts cancer progression in the context of the intact immune system is unknown. Here we report that while inhibiting cancer growth in immunocompromised mice, MR reduces T cell abundance, exacerbates tumour growth and impairs tumour response to immunotherapy in immunocompetent male and female mice. Mechanistically, MR reduces microbial production of hydrogen sulfide, which is critical for immune cell survival/activation. Dietary supplementation of a hydrogen sulfide donor or a precursor, or methionine, stimulates antitumour immunity and suppresses tumour progression. Our findings reveal an unexpected negative interaction between MR, sulfur deficiency and antitumour immunity and further uncover a vital role of gut microbiota in mediating this interaction. Our study suggests that any possible anticancer benefits of MR require careful consideration of both the microbiota and the immune system.

Impact of clomazone on bacterial communities in two soils

Introduction

Bacterial communities are important for soil functions, but the effect of clomazone on network complexity, composition, and stability is not well studied.

Method

In this study, two agricultural soils were used to test the impact of clomazone on bacterial communities, and the two soils were treated with three concentrations of clomazone (0, 0.8, 8, and 80 mg kg1) in an incubator.

Results and discussion

Bacterial network nodes, links, and average degrees were all decreased by 9-384, 648-829, and 0.703-2.429, respectively. Based on keystone nodes, the topological roles of the nodes were also influenced by clomazone. Bacterial network composition was also impacted based on the analysis of similarity (ANOSIM) and network dissimilarity. Compared with control and clomazone treatments in both soils, the ANOSIM between control and all clomazone treatments was higher than 0.6, network dissimilarities were 0.97-0.98, shared nodes were 131-260, and shared links were 12-100. The bacterial network stability was decreased by clomazone, with decreased robustness by 0.01-0.016 and increased vulnerability by 0.00023-0.00147 in both soils. There were fewer bacterial network modules preserved after clomazone treatment, and the bacterial network community functions were also impacted in both soils. Based on these results, soil bacterial species connections, modularization, and network stability were significantly impacted by clomazone.

Tumorigenesis in Inflammatory Bowel Disease: Microbiota-Environment Interconnections

Colo-rectal cancer (CRC) is undoubtedly one of the most severe complications of inflammatory bowel diseases (IBD). While sporadic CRC develops from a typical adenoma-carcinoma sequence, IBD-related CRC follows different and less understood pathways and its pathophysiological mechanisms were not completely elucidated. In contrast to chronic inflammation, which is nowadays a well-recognised drive towards neoplastic transformation in IBD, only recently was gut microbiota demonstrated to interfere with both inflammation processes and immune-mediated anticancer surveillance. Moreover, the role of microbiota appears particularly complex and intriguing when also considering its multifaceted interactions with multiple environmental stimuli, notably chronic pathologies such as diabetes and obesity, lifestyle (diet, smoking) and vitamin intake. In this review, we presented a comprehensive overview on current evidence of the influence of gut microbiota on IBD-related CRC, in particular its mutual interconnections with the environment.

Clomazone impact on fungal network complexity and stability

Introduction

Soil fungal network composition and stability are important for soil functions, but there is less understanding of the impact of clomazone on network complexity and stability.

Methods

In this work, two agricultural soils were used to investigate the impact of clomazone on fungal network complexity, composition, and stability. The two soils were treated with clomazone solution (0, 0.8, 8, and 80  mg kg^-1) and kept in an incubator.

Results and Discussion

Under the influence of clomazone, the fungal network nodes were decreased by 12-42; however, the average degree was increased by 0.169-1.468 and fungal network density was increased by 0.003-0.054. The keystone nodes were significantly changed after clomazone treatment. Network composition was also impacted. Specifically, compared with control and clomazone treatments in both soils, the shared edges were fewer than 54 in all comparisons, and network dissimilarity was 0.97-0.98. These results suggested that fungal network composition was significantly impacted. The network robustness was increased by 0.0018-0.0209, and vulnerability was decreased by 0.00018-0.00059 in both soils, which indicated that fungal network stability was increased by clomazone. In addition, the functions of network communities were also changed in both soils. These results indicated that clomazone could significantly impact soil fungal networks.

Understanding the microbial fibre degrading communities & processes in the equine gut

The equine gastrointestinal tract is a self-sufficient fermentation system, housing a complex microbial consortium that acts synergistically and independently to break down complex lignocellulolytic material that enters the equine gut. Despite being strict herbivores, equids such as horses and zebras lack the diversity of enzymes needed to completely break down plant tissue, instead relying on their resident microbes to carry out fibrolysis to yield vital energy sources such as short chain fatty acids. The bulk of equine digestion occurs in the large intestine, where digesta is fermented for 36-48 h through the synergistic activities of bacteria, fungi, and methanogenic archaea. Anaerobic gut dwelling bacteria and fungi break down complex plant polysaccharides through combined mechanical and enzymatic strategies, and notably possess some of the greatest diversity and repertoire of carbohydrate active enzymes among characterized microbes. In addition to the production of enzymes, some equid-isolated anaerobic fungi and bacteria have been shown to possess cellulosomes, powerful multi-enzyme complexes that further enhance break down. The activities of both anaerobic fungi and bacteria are further facilitated by facultatively aerobic yeasts and methanogenic archaea, who maintain an optimal environment for fibrolytic organisms, ultimately leading to increased fibrolytic microbial counts and heightened enzymatic activity. The unique interactions within the equine gut as well as the novel species and powerful mechanisms employed by these microbes makes the equine gut a valuable ecosystem to study fibrolytic functions within complex communities. This review outlines the primary taxa involved in fibre break down within the equine gut and further illuminates the enzymatic strategies and metabolic pathways used by these microbes. We discuss current methods used in analysing fibrolytic functions in complex microbial communities and propose a shift towards the development of functional assays to deepen our understanding of this unique ecosystem.

Effects of Starch Overload and Cecal Buffering on Fecal Microbiota of Horses

Starch overload in horses causes gastrointestinal and metabolic disorders that are associated with microbiota changes. Therefore, we identified the fecal microbiota and hypothesized that intracecal injection of alkaline solution (buffer; Mg(OH)2 + Al(OH)3) could stabilize these microbiota and clinical changes in horses submitted to corn starch overload. Ten crossbred horses (females and geldings) were allocated to group I (water−saline and starch−buffer treatments) and group II (water−buffer and starch−saline treatments). Clinical signs, gross analysis of the feces, and fecal microbiota were evaluated through 72 h (T0; T8; T12; T24; T48; T72). Corn starch or water were administrated by nasogastric tube at T0, and the buffer injected into the cecum at T8 in starch−buffer and water−buffer treatments. Starch overload reduced the richness (p < 0.001) and diversity (p = 0.001) of the fecal microbiota. However, the starch−buffer treatment showed greater increase in amylolytic bacteria (Bifidobacterium 0.0% to 5.6%; Lactobacillus 0.1% to 7.4%; p < 0.05) and decrease in fibrolytic bacteria (Lachnospiraceae 10.2% to 5.0%; Ruminococcaceae 11.7% to 4.2%; p < 0.05) than starch−saline treatment. Additionally, animals that received starch−buffer treatment showed more signs of abdominal discomfort and lameness associated with dysbiosis (amylolytic r > 0.5; fribolytic r < 0.1; p < 0.05), showing that cecal infusion of buffer did not prevent, but intensified intestinal disturbances and the risk of laminitis.

How Dietary Fibre, Acting via the Gut Microbiome, Lowers Blood Pressure

PURPOSE OF REVIEW

To discuss the interplay behind how a high-fibre diet leads to lower blood pressure (BP) via the gut microbiome.

RECENT FINDINGS

Compelling evidence from meta-analyses support dietary fibre prevents the development of cardiovascular disease and reduces BP. This relation is due to gut microbial metabolites, called short-chain fatty acids (SCFAs), derived from fibre fermentation. The SCFAs acetate, propionate and butyrate lower BP in independent hypertensive models. Mechanisms are diverse but still not fully understood-for example, they include G protein-coupled receptors, epigenetics, immune cells, the renin-angiotensin system and vasculature changes. Lack of dietary fibre leads to changes to the gut microbiota that drive an increase in BP. The mechanisms involved are unknown. The intricate interplay between fibre, the gut microbiota and SCFAs may represent novel therapeutic approaches for high BP. Other gut microbiota-derived metabolites, produced when fibre intake is low, may hold potential therapeutic applications. Further translational evidence is needed.

Bacterial Keystone Taxa Regulate Carbon Metabolism in the Earthworm Gut

As important ecosystem engineers in soils, earthworms strongly influence carbon cycling through their burrowing and feeding activities. Earthworms do not perform these roles in isolation, because their intestines create a special habitat favorable for complex bacterial communities. However, how the ecological functioning of these earthworm-microbe interactions regulates carbon cycling remains largely unknown. To fill this knowledge gap, we investigated the bacterial community structure and carbon metabolic activities in the intestinal contents of earthworms and compared them to those of the adjacent soils in a long-term fertilization experiment. We discovered that earthworms harbored distinct bacterial communities compared to the surrounding soil under different fertilization conditions. The bacterial diversity was significantly larger in the adjacent soils than that in the earthworm gut. Three statistically identified keystone taxa in the bacterial networks, namely, Solirubrobacterales, Ktedonobacteraceae, and Jatrophihabitans, were shared across the earthworm gut and adjacent soil. Environmental factors (pH and organic matter) and keystone taxa were important determinants of the bacterial community composition in the earthworm gut. Both PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) and FAPROTAX (Functional Annotation of Prokaryotic Taxa) predicted that carbon metabolism was significantly higher in adjacent soil than in the earthworm gut, which was consistent with the average well color development obtained by the Biolog assay. Structural equation modeling combined with correlation analysis suggested that pH, organic matter, and potential keystone taxa exhibited significant relationships with carbon metabolism. This study deepens our understanding of the mechanisms underlying keystone taxa regulating carbon cycling in the earthworm gut. IMPORTANCE The intestinal microbiome of earthworms is a crucial component of the soil microbial community and nutrient cycling processes. If we could elucidate the role of this microbiome in regulating soil carbon metabolism, we would make a crucial contribution to understanding the ecological role of these gut bacterial taxa and to promoting sustainable agricultural development. However, the ecological functioning of these earthworm-microbe interactions in regulating carbon cycling has so far not been fully investigated. In this study, we revealed, first, that the bacterial groups of Solirubrobacterales, Ktedonobacteraceae, and Jatrophihabitans were core keystone taxa across the earthworm gut and adjacent soil and, second, that the environmental factors (pH and organic carbon) and keystone taxa strongly affected the bacterial community composition and exhibited close correlations with microbial carbon metabolism. Our results provide new insights into the community assembly of the earthworm gut microbiome and the ecological importance of potential keystone taxa in regulating carbon cycling dynamics.

Short Chain Fatty Acids and Bacterial Taxa Associated with Reduced Salmonella enterica serovar I 4,[5],12:i:- Shedding in Swine Fed a Diet Supplemented with Resistant Potato Starch

Salmonella enterica serovar I 4,[5],12:i:- is a foodborne pathogen of concern because many isolates are multidrug-resistant (resistant to ≥3 antimicrobial classes) and metal tolerant. In this study, three in-feed additives were individually tested for their ability to reduce Salmonella I 4,[5],12:i:- shedding in swine: resistant potato starch (RPS), high amylose corn starch, and a fatty acid blend, compared with a standard control diet over 21 days. Only RPS-fed pigs exhibited a reduction in Salmonella fecal shedding, different bacterial community compositions, and different cecal short chain fatty acid (SCFA) profiles relative to control animals. Within the RPS treatment group, pigs shedding the least Salmonella tended to have greater cecal concentrations of butyrate, valerate, caproate, and succinate. Additionally, among RPS-fed pigs, several bacterial taxa (Prevotella_7, Olsenella, and Bifidobacterium, and others) exhibited negative relationships between their abundances of and the amount of Salmonella in the feces of their hosts. Many of these same taxa also had significant positive associations with cecal concentrations of butyrate, valerate, caproate, even though they are not known to produce these SCFAs. Together, these data suggest the RPS-associated reduction in Salmonella shedding may be dependent on the establishment of bacterial cross feeding interactions that result in the production of certain SCFAs. However, directly feeding a fatty acid mix did not replicate the effect. RPS supplementation could be an effective means to reduce multidrug-resistant (MDR) S. enterica serovar I 4,[5],12:i:- in swine, provided appropriate bacterial communities are present in the gut. IMPORTANCE Prebiotics, such as resistant potato starch (RPS), are types of food that help to support beneficial bacteria and their activities in the intestines. Salmonella enterica serovar I 4,[5],12:i:- is a foodborne pathogen that commonly resides in the intestines of pigs without disease, but can make humans sick if unintentionally consumed. Here we show that in Salmonella inoculated pigs, feeding them a diet containing RPS altered the colonization and activity of certain beneficial bacteria in a way that reduced the amount of Salmonella in their feces. Additionally, within those fed RPS, swine with higher abundance of these types of beneficial bacteria had less Salmonella I 4,[5],12:i:- in their feces. This work illustrates likely synergy between the prebiotic RPS and the presence of certain gut microorganisms to reduce the amount of Salmonella in the feces of pigs and therefore reduce the risk that humans will become ill with MDR Salmonella serovar I 4,[5],12:i:-.

Plant diversity enhances soil fungal network stability indirectly through the increase of soil carbon and fungal keystone taxa richness

Plant diversity is critical to the stability of ecosystems. However, our knowledge about the plant diversity effect on the stability of belowground communities is limited. Here, we characterized soil fungal diversity and co-occurrence network across a plant diversity gradient in a diversity manipulation experiment. We found that higher plant diversity resulted in higher fungal diversity, network complexity and stability. The positive plant diversity effect on fungal network stability was indirect via the increase of soil carbon and fungal keystone taxa richness based on structural equation modeling analysis. The model explained 44% variations of network stability when combining soil carbon and fungal keystone taxa richness, but explained approximate 30% variations of network stability when considering either one of the two factors, indicating that environmental filtering and biotic interaction processes play comparable roles in mediating the plant diversity effect on soil fungal network stability. The plant diversity-induced fungal network stability was significantly correlated with community-level functions including community resistance and enzyme activities. This study, from the view of networks, provides new insights into the plant diversity effect on the stability of soil microbial communities, which have implications for biodiversity conservation and policy development.

Phytoremediation of cadmium-contaminated sediment using Hydrilla verticillata and Elodea canadensis harbor two same keystone rhizobacteria Pedosphaeraceae and Parasegetibacter

Aquatic macrophytes have been widely employed for in-situ phytoremediation of cadmium (Cd) polluted sediments. But, little is known about the responses of rhizosphere bacteria and their interspecific interactions to phytoremediation. In this study, the α-diversity, community composition, co-occurrence network and keystone species of sediment bacteria in rhizosphere zones of two typical macrophytes, Hydrilla verticillata and Elodea canadensis, were investigated using 16S rRNA gene high-throughput sequencing. The results showed that after fifty days of phytoremediation, a group of specialized sediment bacteria were assembled in the rhizosphere zones closely associated with different host macrophytes. Rhizosphere micro-environments, i.e., the increases of redox potential and organic matter and the decreases of pH, nitrogen and phosphorus, reduced bacterial α-diversity through niche-based species-sorting process, which in turn reduced interspecific mutualistic relationships. But meanwhile, benefiting from the nutrients supplied from macrophyte roots, more bacterial species survived in the highly Cd-contaminated sediments (50 mg kg^-1). In addition, the co-occurrence network revealed that both macrophytes harbored two same keystone bacteria with the high betweenness centrality values, including the family Pedosphaeraceae (genus_unclassified) and genus Parasegetibacter. Their relative abundances were up to 28-fold and 25-fold higher than other keystone species, respectively. Furthermore, these two keystone bacteria were metabolic generalists with vital ecological functions, which posed significant potentials for promoting plant growth and tolerating Cd bio-toxicity. Therefore, the identified keystone rhizobacteria, Pedosphaeraceae and Parasegetibacter, would be potential microbial modulations applied for the future optimization of phytoremediation in Cd-contaminated sediment.

Concepts and Consequences of a Core Gut Microbiota for Animal Growth and Development

Animal microbiomes are occasionally considered as an extension of host anatomy, physiology, and even their genomic architecture. Their compositions encompass variable and constant portions when examined across multiple hosts. The latter, termed the core microbiome, is viewed as more accommodated to its host environment and suggested to benefit host fitness. Nevertheless, discrepancies in its definitions, characteristics, and importance to its hosts exist across studies. We survey studies that characterize the core microbiome, detail its current definitions and available methods to identify it, and emphasize the crucial need to upgrade and standardize the methodologies among studies. We highlight ruminants as a case study and discuss the link between the core microbiome and host physiology and genetics, as well as potential factors that shape it. We conclude with main directives of action to better understand the host-core microbiome axis and acquire the necessary insights into its controlled modulation. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Fostering next-generation probiotics in human gut by targeted dietary modulation: An emerging perspective

Emerging evidence and an in-depth understanding of the microbiome have helped in identifying beneficial commensals and their therapeutic potentials. Specific commensal taxa/ strains of the human gut microbiome have been positively associated with human health and recently termed as next-generation probiotics (NGPs). Of these, Akkermansia muciniphila, Ruminococcus bromii, Faecalibacterium prausnitzii, Anaerobutyricum hallii, and Roseburia intestinalis are the five most relevant gut-derived NGPs that have demonstrated therapeutic potential in managing metabolic diseases. Specific and natural dietary interventions can modulate the abundance and activity of these beneficial bacteria in the gut. Hence, the understanding of targeted stimulation of specific NGP by specific probiotic-targeted diets (PTD) is indispensable for the rational application of their combination. The supplementation of NGP with its specific PTD will help the strain(s) to compete with harmful microbes and acquire its niche. This combination would enhance the effectiveness of NGPs to be used as "live biotherapeutic products" or food nutraceuticals. Under the current milieu, we review various PTDs that influence the abundance of specific potential NGPs, and contemplates potential interactions between diet, microbes, and their effects on host health. Taking into account the study mentioned, we propose that combining NGPs will provide an alternate solution for developing the new diet in conjunction with PTD.

Dietary fibres and IBS: translating functional characteristics to clinical value in the era of personalised medicine

Clinical guidelines in the use of fibre supplementation for patients with IBS provide one-size-fits-all advice, which has limited value. This narrative review addresses data and concepts around the functional characteristics of fibre and subsequent physiological responses induced in patients with IBS with a view to exploring the application of such knowledge to the precision use of fibre supplements. The key findings are that first, individual fibres elicit highly distinct physiological responses that are associated with their functional characteristics rather than solubility. Second, the current evidence has focused on the use of fibres as a monotherapy for IBS symptoms overall without attempting to exploit these functional characteristics to elicit specific, symptom-targeted effects, or to use fibre types as adjunctive therapies. Personalisation of fibre therapies can therefore target several therapeutic goals. Proposed goals include achieving normalisation of bowel habit, modulation of gut microbiota function towards health and correction of microbial effects of other dietary therapies. To put into perspective, bulking fibres that are minimally fermented can offer utility in modulating indices of bowel habit; slowly fermented fibres may enhance the activities of the gut microbiota; and the combination of both fibres may potentially offer both benefits while optimising the activities of the microbiota throughout the different regions of the colon. In conclusion, understanding the GI responses to specific fibres, particularly in relation to the physiology of the individual, will be the future for personalising fibre therapy for enhancing the personalised management of patients with IBS.

Effect of a Polyphenol-Based Additive in Pig Diets in the Early Stages of Growth

The weaning period is a stressful period for the gastrointestinal tract (GIT) of piglets. This work aims to evaluate the effects of the commercial polyphenol-based product GreenFIS^® on: (1) GIT health and performance of 60 weaned piglets; (2) digestibility in 18 growing pigs. Three diets were tested: a control diet (C), C plus 2.5 g of GreenFIS^®/kg C (T1), and C plus 5 g of GreenFIS^®/kg C (T2). After the post-weaning trial three piglets per treatment were sacrificed for the GIT histological analysis. No differences between diets were recorded in terms of growing performance or clinical and biochemical blood parameters. The GIT histological analysis did not show any indicators of inflammation for any of the groups. The feces of the two extreme treatments (C and T2) were analyzed for microbiota, revealing a greater presence of the Ruminococcus bromii group, positively associated with starch degradation, in T2. In the second experiment six pigs per treatment were randomly chosen for the digestibility study. The inclusion of GreenFIS^® at both levels led to a higher fecal digestibility of gross energy (86.2%, 89.1%, and 89.5%, for C, T1, and T2, respectively) and crude protein (87.0%, 90.2%, and 90.0%). In conclusion, the additive did not improve, in the excellent experimental hygienic conditions, the gut health, but it did increase nutrient digestibility.

Dietary fibre complexity and its influence on functional groups of the human gut microbiota

The aim of this review is to provide an overview of the complex interactions between dietary fibre and the resident microbial community in the human gut. The microbiota influences both health maintenance and disease development. In the large intestine, the microbiota plays a crucial role in the degradation of dietary carbohydrates that remain undigested in the upper gut (non-digestible carbohydrates or fibre). Dietary fibre contains a variety of different types of carbohydrates, and its breakdown is facilitated by many different microbial enzymes. Some microbes, termed generalists, are able to degrade a range of different carbohydrates, whereas others are more specialised. Furthermore, the physicochemical characteristics of dietary fibre, such as whether it enters the gut in soluble or insoluble form, also likely influence which microbes can degrade it. A complex nutritional network therefore exists comprising primary degraders able to attack complex fibre and cross feeders that benefit from fibre breakdown intermediates or fermentation products. This leads predominately to the generation of the short-chain fatty acids (SCFA) acetate, propionate and butyrate, which exert various effects on host physiology, including the supply of energy, influencing glucose and lipid metabolism and anti-carcinogenic and anti-inflammatory actions. In order to effectively modulate the gut microbiota through diet, there is a need to better understand the complex competitive and cooperative interactions between gut microbes in dietary fibre breakdown, as well as how gut environmental factors and the physicochemical state of fibre originating from different types of diets influence microbial metabolism and ecology in the gut.

Starch Microspheres Entrapped with Chitosan Delay In Vitro Fecal Fermentation and Regulate Human Gut Microbiota Composition

A slow dietary fiber fermentation rate is desirable to obtain a steady metabolite release and even distribution throughout the entire colon, ensuring to meet the energy needs in the distal colon. In this study, we prepared starch-entrapped microspheres with a variable chitosan-to-starch ratio by means of electrospraying and investigated the fermentability by human fecal microbiota in an in vitro batch system. Starch encapsulation reduced microbial gas production and the concentration of short-chain fatty acids. Butyrate production, in particular, gradually decreased with increasing chitosan proportions. Moreover, the starch and chitosan composites induced a synergistic effect on the gut microbiota composition. Roseburia, Lachnospiraceae, and Clostridiales were promoted by all of the microspheres, and the abundance of the aforementioned health-promoting taxa reached a maximum in chitosan/starch microspheres with a 1:6 (w/w) ratio. Our findings highlight the possible benefits of rationally designing functional foods targeting functional and taxonomic gut microbiota modulation.

Calling for a systems approach in microbiome research and innovation

Microbiomes are all around us in natural and cultivated ecosystems, for example, soils, plants, animals and our own body. Microbiomes are essential players of biotechnological applications, and their functions drive human, animal, plant and environmental health. The rapidly developing microbiome research landscape was studied by a global mapping excercise and bibliometric analysis. Although microbiome research is performed in many different science fields, using similar concepts within and across fields, microbiomes are mostly investigated one ecosystem at-a-time. In order to fully understand microbiome impacts and leverage microbial functions, research needs to adopt a systems approach connecting microbiomes and research initiatives in divergent fields to create understanding on how microbiomes can be modulated for desirable functions as a basis of sustainable, circular bioeconomy.

Spatial and Temporal Distribution of Bacterioplankton Molecular Ecological Networks in the Yuan River under Different Human Activity Intensity

Bacterioplankton communities play a crucial role in freshwater ecosystem functioning, but it is unknown how co-occurrence networks within these communities respond to human activity disturbances. This represents an important knowledge gap because changes in microbial networks could have implications for their functionality and vulnerability to future disturbances. Here, we compare the spatiotemporal and biogeographical patterns of bacterioplankton molecular ecological networks using high-throughput sequencing of Illumina HiSeq and multivariate statistical analyses from a subtropical river during wet and dry seasons. Results demonstrated that the lower reaches (high human activity intensity) network had less of an average degree (10.568/18.363), especially during the dry season, when compared with the upper reaches (low human activity intensity) network (10.685/37.552) during the wet and dry seasons, respectively. The latter formed more complexity networks with more modularity (0.622/0.556) than the lower reaches (high human activity intensity) network (0.505/0.41) during the wet and dry seasons, respectively. Bacterioplankton molecular ecological network under high human activity intensity became significantly less robust, which is mainly caused by altering of the environmental conditions and keystone species. Human activity altered the composition of modules but preserved their ecological roles in the network and environmental factors (dissolved organic carbon, temperature, arsenic, oxidation-reduction potential and Chao1 index) were the best parameters for explaining the variations in bacterioplankton molecular ecological network structure and modules. Proteobacteria, Actinobacteria and Bacteroidetes were the keystone phylum in shaping the structure and niche differentiations in the network. In addition, the lower reaches (high human activity intensity) reduce the bacterioplankton diversity and ecological niche differentiation, which deterministic processes become more important with increased farmland and constructed land area (especially farmland) with only 35% and 40% of the community variation explained by the neutral community model during the wet season and dry season, respectively. Keystone species in high human activity intensity stress habitats yield intense functional potentials and Bacterioplankton communities harbor keystone taxa in different human activity intensity stress habitats, which may exert their influence on microbiome network composition regardless of abundance. Therefore, human activity plays a crucial role in shaping the structure and function of bacterioplankton molecular ecological networks in subtropical rivers and understanding the mechanisms of this process can provide important information about human-water interaction processes, sustainable uses of freshwater as well as watershed management and conservation.

The Athlete and Gut Microbiome: Short-chain Fatty Acids as Potential Ergogenic Aids for Exercise and Training

Short-chain fatty acids (SCFAs) are metabolites produced in the gut via microbial fermentation of dietary fibers referred to as microbiota-accessible carbohydrates (MACs). Acetate, propionate, and butyrate have been observed to regulate host dietary nutrient metabolism, energy balance, and local and systemic immune functions. In vitro and in vivo experiments have shown links between the presence of bacteria-derived SCFAs and host health through the blunting of inflammatory processes, as well as purported protection from the development of illness associated with respiratory infections. This bank of evidence suggests that SCFAs could be beneficial to enhance the athlete's immunity, as well as act to improve exercise recovery via anti-inflammatory activity and to provide additional energy substrates for exercise performance. However, the mechanistic basis and applied evidence for these relationships in humans have yet to be fully established. In this narrative review, we explore the existing knowledge of SCFA synthesis and the functional importance of the gut microbiome composition to induce SCFA production. Further, changes in gut microbiota associated with exercise and various dietary MACs are described. Finally, we provide suggestions for future research and practical applications, including how these metabolites could be manipulated through dietary fiber intake to optimize immunity and energy metabolism.

Structure and substrate recognition by the Ruminococcus bromii amylosome pullulanases

Pullulanases are glycoside hydrolase family 13 (GH13) enzymes that target α1,6 glucosidic linkages within starch and aid in the degradation of the α1,4- and α1,6- linked glucans pullulan, glycogen and amylopectin. The human gut bacterium Ruminococcus bromii synthesizes two extracellular pullulanases, Amy10 and Amy12, that are incorporated into the multiprotein amylosome complex that enables the digestion of granular resistant starch from the diet. Here we provide a comparative biochemical analysis of these pullulanases and the x-ray crystal structures of the wild type and the nucleophile mutant D392A of Amy12 complexed with maltoheptaose and 6³-α-D glucosyl-maltotriose. While Amy10 displays higher catalytic efficiency on pullulan and cleaves only α1,6 linkages, Amy12 has some activity on α1,4 linkages suggesting that these enzymes are not redundant within the amylosome. Our structures of Amy12 include a mucin-binding protein (MucBP) domain that follows the C-domain of the GH13 fold, an atypical feature of these enzymes. The wild type Amy12 structure with maltoheptaose captured two oligosaccharides in the active site arranged as expected following catalysis of an α1,6 branch point in amylopectin. The nucleophile mutant D392A complexed with maltoheptaose or 6³-α-D glucosyl-maltotriose captured β-glucose at the reducing end in the -1 subsite, facilitated by the truncation of the active site aspartate and stabilized by stacking with Y279. The core interface between the co-crystallized ligands and Amy12 occurs within the -2 through + 1 subsites, which may allow for flexible recognition of α1,6 linkages within a variety of starch structures.

Synergistic Effects of the Jackfruit Seed Sourced Resistant Starch and Bifidobacterium pseudolongum subsp. globosum on Suppression of Hyperlipidemia in Mice

Approximately 17 million people suffer from cardiovascular diseases caused by hyperlipidemia, making it a serious global health concern. Among others, resistant starch (RS) has been widely used as a prebiotic in managing hyperlipidemia conditions. However, some studies have reported limited effects of RS on body weight and blood lipid profile of the host, suggesting further investigation on the synergistic effects of RS in combination with probiotics as gut microbes plays a role in lipid metabolism. This study evaluated the effects of jackfruit seed sourced resistant starch (JSRS) as a novel RS on mice gut microbes and hyperlipidemia by performing 16s rRNA and shotgun metagenomic sequencing. The results showed that 10% JSRS had a limited preventive effect on bodyweight and serum lipid levels. However, the JSRS promoted the growth of Bifidobacterium pseudolongum, which indicated the ability of B. pseudolongum for JSRS utilization. In the validation experiment, B. pseudolongum interacted with JSRS to significantly reduce bodyweight and serum lipid levels and had a therapeutic effect on hepatic steatosis in mice. Collectively, this study revealed the improvements of hyperlipidemia in mice by the synergistic effects of JSRS and B. pseudolongum, which will help in the development of “synbiotics” for the treatment of hyperlipidemia in the future.

Alteration of the gut fecal microbiome in children living with HIV on antiretroviral therapy in Yaounde, Cameroon

Multiple factors, such as immune disruption, prophylactic co-trimoxazole, and antiretroviral therapy, may influence the structure and function of the gut microbiome of children infected with HIV from birth. In order to understand whether HIV infection altered gut microbiome and to relate changes in microbiome structure and function to immune status, virological response and pediatric ART regimens, we characterized the gut microbiome of 87 HIV-infected and 82 non-exposed HIV-negative children from Yaounde, a cosmopolitan city in Cameroon. We found that children living with HIV had significantly lower alpha diversity in their gut microbiome and altered beta diversity that may not be related to CD4+ T cell count or viral load. There was an increased level of Akkermansia and Faecalibacterium genera and decreased level of Escherichia and other Gamma proteobacteria in children infected with HIV, among other differences. We noted an effect of ethnicity/geography on observed gut microbiome composition and that children on ritonavir-boosted protease inhibitor (PI/r)-based ART had gut microbiome composition that diverged more from HIV-negative controls compared to those on non-nucleoside reverse-transcriptase inhibitors-based ART. Further studies investigating the role of this altered gut microbiome in increased disease susceptibility are warranted for individuals who acquired HIV via mother-to-child transmission.

The role of short-chain fatty acids in the interplay between gut microbiota and diet in cardio-metabolic health

The gut microbiota plays an important role in cardio-metabolic diseases with diet being among the strongest modulators of gut microbiota composition and function. Resistant dietary carbohydrates are fermented to short-chain fatty acids (SCFAs) by the gut bacteria. Fiber and omega-3 rich diets increase SCFAs production and abundance of SCFA-producing bacteria. Likewise, SCFAs can improve gut barrier integrity, glucose, and lipid metabolism, regulate the immune system, the inflammatory response, and blood pressure. Therefore, targeting the gut microbiota with dietary strategies leading to increased SCFA production may benefit cardio-metabolic health. In this review, we provide an overview of the association between diet, SCFAs produced by the gut microbiota and cardio-metabolic diseases. We first discuss the association between the human gut microbiota and cardio-metabolic diseases, then investigate the role of SCFAs and finally explore the beneficial effects of specific dietary interventions that can improve cardio-metabolic outcomes through boosting the SCFA production.

Intestinal Inflammation as a Dysbiosis of Energy Procurement: New Insights into an Old Topic

Inflammatory bowel disease (IBD) coincides with profound shifts in microbiota and host metabolic energy supply and demand. The gastrointestinal epithelium is anatomically positioned to provide a selective barrier between the anaerobic luminal microbiota and host lamina propria, with the microbiota and epithelium participating in an intricate energy exchange necessary for homeostasis. Maintenance and restoration of the barrier requires high energy flux and places significant demands on available substrates to generate ATP. It is recently appreciated that components of the microbiota contribute significantly to a multitude of biochemical pathways within and outside of the mucosa. Decades-old studies have appreciated that byproducts of the microbiota provide essential sources of energy to the intestinal epithelium, especially the colon. More recent work has unveiled the existence of numerous microbial-derived metabolites that support energy procurement within the mucosa. It is now appreciated that disease-associated shifts in the microbiota, termed dysbiosis, places significant demands on energy acquisition within the mucosa. Here, we review the topic of host- and microbial-derived components that influence tissue energetics in health and during disease.

Resistant starch, microbiome, and precision modulation

Resistant starch, microbiome, and precision modulation. Mounting evidence has positioned the gut microbiome as a nexus of health. Modulating its phylogenetic composition and function has become an attractive therapeutic prospect. Resistant starches (granular amylase-resistant α-glycans) are available as physicochemically and morphologically distinguishable products. Attempts to leverage resistant starch as microbiome-modifying interventions in clinical studies have yielded remarkable inter-individual variation. Consequently, their utility as a potential therapy likely depends predominantly on the selected resistant starch and the subject's baseline microbiome. The purpose of this review is to detail i) the heterogeneity of resistant starches, ii) how resistant starch is sequentially degraded and fermented by specialized gut microbes, and iii) how resistant starch interventions yield variable effects on the gut microbiome.

Synthetic gut microbiome: Advances and challenges

An exponential rise in studies regarding the association among human gut microbial communities, human health, and diseases is currently attracting the attention of researchers to focus on human gut microbiome research. However, even with the ever-growing number of studies on the human gut microbiome, translation into improved health is progressing slowly. This hampering is due to the complexities of the human gut microbiome, which is composed of >1,000 species of microorganisms, such as bacteria, archaea, viruses, and fungi. To overcome this complexity, it is necessary to reduce the gut microbiome, which can help simplify experimental variables to an extent, such that they can be deliberately manipulated and controlled. Reconstruction of synthetic or established gut microbial communities would make it easier to understand the structure, stability, and functional activities of the complex microbial community of the human gut. Here, we provide an overview of the developments and challenges of the synthetic human gut microbiome, and propose the incorporation of multi-omics and mathematical methods in a better synthetic gut ecosystem design, for easy translation of microbiome information to therapies.

Communal living: glycan utilization by the human gut microbiota

Our lower gastrointestinal tract plays host to a vast consortium of microbes, known as the human gut microbiota (HGM). The HGM thrives on a complex and diverse range of glycan structures from both dietary and host sources, the breakdown of which requires the concerted action of cohorts of carbohydrate-active enzymes (CAZymes), carbohydrate-binding proteins, and transporters. The glycan utilization profile of individual taxa, whether 'specialist' or 'generalist', is dictated by the number and functional diversity of these glycan utilization systems. Furthermore, taxa in the HGM may either compete or cooperate in glycan deconstruction, thereby creating a complex ecological web spanning diverse nutrient niches. As a result, our diet plays a central role in shaping the composition of the HGM. This review presents an overview of our current understanding of glycan utilization by the HGM on three levels: (i) molecular mechanisms of individual glycan deconstruction and uptake by key bacteria, (ii) glycan-mediated microbial interactions, and (iii) community-scale effects of dietary changes. Despite significant recent advancements, there remains much to be discovered regarding complex glycan metabolism in the HGM and its potential to affect positive health outcomes.

Effect of pineapple stem starch feeding on rumen microbial fermentation, blood lipid profile, and growth performance of fattening cattle

Pineapple stem starch (PS) was evaluated for its suitability as a new starch source in concentrate for fattening cattle, based on the growth performance, blood profile, and rumen parameters of 36 steers in a 206-day feeding study. PS was formulated as a 40% concentrate and fed with forage in comparison with ground corn (GC) and ground cassava (CA) formulated at the same level. PS feeding improved weight gain and feed conversion ratio without affecting feed intake. PS did not obviously influence blood lipid profiles throughout the experiment. Ruminal concentration of total short-chain fatty acids (SCFA) increased with PS without affecting SCFA composition throughout the feeding study. Rumen amylolytic group, especially Ruminococcus bromii, was dominant in the rumen microbial community, and showed increased abundance by PS feeding throughout the experiment. These results clearly indicate the potential of PS as a useful starch source for fattening cattle in terms of rumen fermentation and growth performance.

Consumption of identically formulated foods extruded under low and high shear force reveals that microbiome redox ratios accompany canine immunoglobulin A production

Digestion-resistant starch (RS) can provide health benefits to the host via gut microbiome-mediated metabolism. This study tested the physiological effects on healthy dogs of identically formulated foods processed under high (n = 16) or low (n = 16) shear extrusion conditions resulting in respective lower and higher levels of RS. Faecal samples collected at weeks 3 and 6 were assayed for stool score, proximate analysis, short-chain fatty acids (SCFA), immunoglobulin A (IgA) and microbiome; faecal metabolome was characterized at week 6. Proximate and digestibility analyses of the foods and stool scores and stool proximate analysis showed few differences between the two shear methods except for increased apparent fibre digestibility in the low shear food. In contrast, levels of butyrate (p = .030) and total SCFA (p = .043) were significantly greater in faeces at week 6 from dogs who consumed the low versus high shear food. Faecal IgA levels were significantly higher at week 3 (p = .001) but not week 6 (p = .110) in the low shear food. Significant differences in 166 metabolites between consumption of the two foods were identified via faecal metabolomic analysis, with changes in sugars, bile acids, advanced glycation end products and few amino acids. Strikingly, consumption of the low shear food resulted in elevated levels of the reduced members of redox couples derived from metabolized sugars and branched-chain and phenyl amino acids. Alpha diversity of the microbiome showed significantly higher species richness in faeces from the low shear group at week 6, though other measures of diversity were similar for both foods. Twelve genus-level operational taxonomic units (OTU; half Firmicutes) significantly differed between the food types. Six OTU significantly correlated with RS-derived sugars and ratios of the redox couples. Taken together, these data show that RS impacts microbiome-mediated metabolism in the gut, resulting in changes in the reducing state.

Longitudinal Investigation of the Gut Microbiota in Goat Kids from Birth to Postweaning

Early microbial colonization in the gut impacts animal performance and lifelong health. However, research on gut microbial colonization and development in young ruminants, especially after weaning, is currently limited. In this study, next-generation sequencing technology was performed to investigate the temporal dynamic changes of the microbial community in the jejunum and colon of goats at 1, 7, 14, 28, 42, 56, 70, and 84 days (d) of age. As age increased, significant increases in microbial diversity, including the number of Observed OTUs and the Shannon Index, were observed in both the jejunum and colon. Regarding beta diversity, significant shifts in community membership and structure from d1 to d84 were observed based on both Bray–Curtis and Jaccard distances. With increasing age, dominant genera in the jejunum shifted from Lactobacillus to unclassified Ruminococcaceae, unclassified Lachnospiraceae and unclassified Clostridiales through starter supplementation, whereas colonic dominant genera changed from Lactobacillus and Butyricicoccus, within d1–d28, to unclassified Ruminococcaceae, unclassified Clostridiales and Campylobacter after solid diet supplementation. The linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed bacterial features that are stage-specific in the jejunum and colon, respectively. In the jejunum and colon, a significantly distinct structure and membership of the microbiota was observed across all ages. The growth stage-associated microbiota in each gut compartment was also identified as a marker for biogeography. Our data indicate the temporal and spatial differences of the gut microbiota in goats are important for their performance and health. Early microbial colonization can influence microbial composition in later life (e.g., post-weaning phase). This study provides insights that the temporal dynamics of gut microbiota development from newborn to post-weaning can aid in developing feeding strategies to improve goat health and production.

Effects of banana powder (Musa acuminata Colla) on the composition of human fecal microbiota and metabolic output using in vitro fermentation

Bananas are rich in indigestible carbohydrates and are considered potential whole-fruit prebiotics. To investigate banana-induced changes in the composition of the human gut microbiota and the production of short chain fatty acids (SCFAs), ripe banana (Musa acuminata Colla, Degrees Brix: 22.6 ± 0.2° Bé), from Hainan, China, was powdered and fermented in vitro for 24 hr with the feces of six Chinese donors. The degradation of banana polysaccharides was observed in all six fecal samples. During in vitro fecal fermentation, banana polysaccharides were gradually degraded up to approximately 80%. The production of SCFAs was also measured. The addition of banana powder increased the concentrations of acetate, propionate, and butyrate, with the production of acetate being higher than that of propionate and butyrate. Changes in the human gut microbiota were assessed using high-throughput sequencing of the 16S ribosomal RNA (rRNA) gene. The results indicated that banana powder significantly altered bacterial diversity, increasing the relative abundance of Bacteroides, while maintaining the proportion of Bifidobacterium in the feces. At the same time, banana powder also increased the proportion of Lactobacillus; however, a significant difference was not observed. In summary, banana powder can be utilized by specific bacteria in human intestines, providing data support for the study of the effects of banana powder on the human intestinal health. PRACTICAL APPLICATION: In this study, in vitro batch fermentation was used to evaluate the effect of banana powder on the human intestinal microbial community, and the metabolized products of banana powder were determined. Our study showed that banana powder improved the human intestinal microbial flora and promoted the growth of Bifidobacterium and Bacteroides and could produce beneficial SCFAs (acetate, propionate, and butyrate). This study provided a theoretical basis for the use of banana powder as a potential prebiotic in production applications and our daily diet.

MetaRNAseq analysis of surti buffalo rumen content reveals that transcriptionally active microorganisms need not be abundant

The present study describes rumen microbiota composition and their functional profiles in Indian Surti buffaloes by metagenomic (MG) and metatranscriptomic (MT) approaches. The study compares samples from buffaloes fed three different proportion of roughages; green and dry type of roughage; and different rumen liquor fractions. Irrespective of sample, Bacteroidetes and Firmicutes were the most predominant bacterial phyla, followed by Proteobacteria, Fibrobacteres and Actinobacteria while, Prevotella, Bacteroides, Ruminococcus and Clostridium were the most abundant genera. Different proportions of taxa were observed in both MG and MT approaches indicating the differences in organisms present and organisms active in the rumen. Higher proportions of fungal taxa were observed in MT while important organisms like Fibrobacter and Butyrivibrio and abundant organisms like Bacteroides and Prevotella were underrepresented in MT data. Functionally, higher proportions of genes involved in Carbohydrate metabolism, Amino acid metabolism and Translation were observed in both data. Genes involved in Metabolism were observed to be underrepresented in MT data while, those involved in Genetic information processing were overrepresented in MT data. Further, genes involved in Carbohydrate metabolism were overexpressed compared to genes involved in Amino acid metabolism in MT data compared to MG data which had higher proportion of genes involved in Amino acid metabolism than Carbohydrate metabolism. In all significant differences were observed between both approaches, different fractions of rumen liquor (liquid and solid) and different proportions of roughage in diet.

Potential prebiotic effect of fruit and vegetable byproducts flour using in vitro gastrointestinal digestion

Fruit and vegetable byproducts (FVBP) present high content of bioactive compounds and dietary fibers and have demonstrated a positive modulatory effect upon gut microbiota composition. In the present study, the prebiotic potential of a FVBP flour obtained from solid byproducts after fruit and vegetable processing was evaluated after in vitro gastrointestinal digestion. An initial screening with three strains of Lactobacillus (Lactobacillus casei 01, Lactobacillus rhamnosus R11 and Lactobacillus acidophilus LA-5®) and one Bifidobacterium strain (Bifidobacterium animalis spp. lactis BB12®) was carried out and then the prebiotic effect of FVBP flour was performed with fecal samples of five donors. The changes in gut microbiota were evaluated at 0, 12, 24 and 48 h of fermentation by the real-time polymerase chain reaction (qPCR) method with 16S rRNA-based specific primers. The pH and short chain fatty acids (SCFA) production at each fermentation time were assessed. The fructooligosaccharides (FOS) were used as positive control. The impact of FVBP flour upon cell viability was also evaluated. FVBP flour showed higher prebiotic effect than FOS on growth enhancement of Lactobacillus after 48 h of fermentation and similar bifidogenic effect as FOS on Bifidobacterium growth at 12, 24 and 48 h of fermentation. SCFA production was observed when FVBP flour was used as carbon source, including butyrate, which supports the prebiotic potential of this flour. Additionally, it was observed that after in vitro gastrointestinal digestion, the FVBP flour at 3% promoted cell metabolism of Caco-2 cell line up to 67%. Thus, the present study demonstrates the viability of using a fruit and vegetable byproducts flour as a potential sustainable prebiotic source.

Consumption of Cooked Black Beans Stimulates a Cluster of Some Clostridia Class Bacteria Decreasing Inflammatory Response and Improving Insulin Sensitivity

There is limited information on the effect of black beans (BB) as a source of protein and resistant starch on the intestinal microbiota. The purpose of the present work was to study the effect of cooked black beans with and without high fat and sugar (HF + S) in the diet on body composition, energy expenditure, gut microbiota, short-chain fatty acids, NF-κB, occluding and insulin signaling in a rat model and the area under the curve for glucose, insulin and incretins in healthy subjects. The consumption of BB reduced the percentage of body fat, the area under the curve of glucose, serum leptin, LPS, glucose and insulin concentrations and increased energy expenditure even in the presence of HF + S. These results could be mediated in part by modification of the gut microbiota, by increasing a cluster of bacteria in the Clostridia class, mainly R. bromii, C. eutactus, R. callidus, R. flavefaciens and B. pullicaecorum and by an increase in the concentration of fecal butyrate. In conclusion, the consumption of BB can be recommended to prevent insulin resistance and metabolic endotoxemia by modifying the gut microbiota. Finally, the groups fed BB showed lower abundance of hepatic FMO-3, even with a high-fat diet protecting against the production of TMAO and obesity.

Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease

Studies of inflammatory bowel disease (IBD) have been inconclusive in relating microbiota with distribution of inflammation. We report microbiota, host transcriptomics, epigenomics and genetics from matched inflamed and non-inflamed colonic mucosa [50 Crohn's disease (CD); 80 ulcerative colitis (UC); 31 controls]. Changes in community-wide and within-patient microbiota are linked with inflammation, but we find no evidence for a distinct microbial diagnostic signature, probably due to heterogeneous host-microbe interactions, and show only marginal microbiota associations with habitual diet. Epithelial DNA methylation improves disease classification and is associated with both inflammation and microbiota composition. Microbiota sub-groups are driven by dominant Enterbacteriaceae and Bacteroides species, representative strains of which are pro-inflammatory in vitro, are also associated with immune-related epigenetic markers. In conclusion, inflamed and non-inflamed colonic segments in both CD and UC differ in microbiota composition and epigenetic profiles.