Microbial interaction between the succinate-utilizing bacterium Phascolarctobacterium faecium and the gut commensal Bacteroides thetaiotaomicron

Species-level verification of Phascolarctobacterium association with colorectal cancer

We have previously demonstrated an association between increased abundance of Phascolarctobacterium and colorectal cancer (CRC) and adenomas in two independent Norwegian cohorts. Here we seek to verify our previous findings using new cohorts and methods. In addition, we characterize lifestyle and sex specificity, the functional potential of the Phascolarctobacterium species, and their interaction with other microbial species. We analyze Phascolarctobacterium with 16S rRNA sequencing, shotgun metagenome sequencing, and species-specific qPCR, using 2350 samples from three Norwegian cohorts-CRCAhus, NORCCAP, and CRCbiome-and a large publicly available data set, curatedMetagenomicData. Using metagenome-assembled genomes from the CRCbiome study, we explore the genomic characteristics and functional potential of the Phascolarctobacterium pangenome. Three species of Phascolarctobacterium associated with adenoma/CRC were consistently detected by qPCR and sequencing. Positive associations with adenomas/CRC were verified for Phascolarctobacterium succinatutens and negative associations were shown for Phascolarctobacterium faecium and adenoma in curatedMetagenomicData. Men show a higher prevalence of P. succinatutens across cohorts. Co-occurrence among Phascolarctobacterium species was low (<6%). Each of the three species shows distinct microbial composition and forms distinct correlation networks with other bacterial taxa, although Dialister invisus was negatively correlated to all investigated Phascolarctobacterium species. Pangenome analyses showed P. succinatutens to be enriched for genes related to porphyrin metabolism and degradation of complex carbohydrates, whereas glycoside hydrolase enzyme 3 was specific to P. faecium.IMPORTANCEUntil now Phascolarctobacterium has been going under the radar as a CRC-associated genus despite having been noted, but overseen, as such for over a decade. We found not just one, but two species of Phascolarctobacterium to be associated with CRC-Phascolarctobacterium succinatutens was more abundant in adenoma/CRC, while Phascolarctobacterium faecium was less abundant in adenoma. Each of them represents distinct communities, constituted by specific microbial partners and metabolic capacities-and they rarely occur together in the same patients. We have verified that P. succinatutens is increased in adenoma and CRC and this species should be recognized among the most important CRC-associated bacteria.

Multi-omics reveals the effects of dietary supplementation with Bupleuri radix branch powder on gut microbiota and lipid metabolism: insights into gut microbial-muscle interactions

Improving livestock growth and raising the quality of livestock products have attracted much attention owing to the market's growing need for livestock products. Bupleuri Radix branches powder (BR) has a variety of health characteristics, but its effects on ruminant growth and animal product quality are still uncertain. This study explored the effects of BR on growth performance, health status, gut microbiota, and muscle lipid metabolism of Shaanxi fine-wool sheep (SFS), and examined the interaction between gut microbiota and lipid metabolism through correlation analysis. The results indicated that BR can regulate the immune function, intestinal VFAs, and enzyme activity of FSF by improving the gut microbiota, thereby affecting its muscle lipid metabolism. The lipid metabolite TG showed a strong positive correlation with the gut microbes Bacteroides and Fibrobacter, while Phosphatidylethanolamine and Phosphatidyl serine (PE and PS) showed a significant negative correlation with Fibrobacter. The above results indicate that gut microbiota and lipid metabolites interact with each other. BR has the effects of promoting SFS growth, improving body health, and improving meat quality. These findings offer new insights into improve animal growth performance and livestock product quality in modern farming.

IMPORTANCE

Enhancing livestock growth performance and improving meat quality are important guidelines for the development of the current animal husbandry industry; thus, we explored a comprehensive study of Bupleuri Radix (BR) on growth performance, gut microbiology, and muscle lipid metabolism in Shaanxi fine-wool sheep (SFS). Our research has found that BR could improve the growth performance of SFS and meat quality by affecting gut microbes. This study provides new solutions to improve the economic efficiency of animal husbandry.

In vitro dynamic digestion properties and fecal fermentation of Dictyophora indusiata polysaccharide: Structural characterization and gut microbiota

The in vitro dynamic digestive model more realistically simulates the human digestive system compared to static digestive model. In this study, the dynamic in vitro stomach-intestine digestive system and fecal fermentation was used to investigate the dynamic digestion properties and fermentation properties of Dictyophora indusiata polysaccharide. The results showed that there were no significant changes in molecular weight, functional groups and surface morphology after the in vitro dynamic simulated digestion, indicating that D. indusiata polysaccharide maintained a relatively stable structure during the dynamic in vitro salivary-gastrointestinal digestion. In addition, D. indusiata polysaccharide improved the abundance of beneficial bacteria, including Blautia, Coprobacter and Fusicatenibacter. It is remarkable that D. indusiata polysaccharide significantly increased the level of acetic acid and propionic acid. In conclusion, these results suggested that D. indusiata polysaccharide was a potential source of prebiotics, which provides a basis for the development of D. indusiata polysaccharide in the food or medical field.

Succinate-mediated symbiosis between Dialister hominis and an uncharacterized Segatella-like pectinophile

OBJECTIVES

Syntrophy has been documented between pectinophiles and methanol-utilizing bacteria, along with instances of cross-feeding between pectinophiles and methanogens. However, studies on the ecology of pectinophiles in anaerobic digestion (AD) are lacking. Therefore, in this study, we aimed to elucidate the ecology of pectinophiles by isolating novel pectinophile forms and conducting a comprehensive analysis of their physiology and ecology.

METHODS

Complex microbial communities from AD systems were enriched in a pectin-containing medium; subsequently, specific strains were isolated using a pectinophile isolation method. The carbon source assimilation and growth ability of the isolates, along with their symbiotic relationships, were evaluated using batch tests.

RESULTS

Strain LPYR103-Pre exhibited 16S rRNA gene sequence similarity and average nucleotide identity values of 94.3 % and 77.9 %, respectively, compared to its closest related species, Segatella cerevisiae. Strain LPYR103-Pre demonstrated attenuated growth in the presence of eight common sugars but exhibited remarkably high growth in the presence of pectin, d-galacturonate, and d-glucuronate, with succinate being identified as a primary metabolite. Accumulation of succinate inhibited the growth of strain LPYR103-Pre. However, this growth impediment was alleviated by Dialister hominis LPYG114-Dih, whose growth required succinate.

CONCLUSIONS

Our results elucidate the specific carbon source requirements of the Segatella-like strain LPYR103-Pre and succinate-mediated symbiosis involving D. hominis. These findings provide new insights into the degradation of pectin and its degradation products during AD, contributing to the identification of unknown pectinophiles.

Regulation of immune responses to food by commensal microbes

The increasing prevalence of immune-mediated non-communicable chronic diseases, such as food allergies, has prompted a deeper investigation into the role of the gut microbiome in modulating immune responses. Here, we explore the complex interactions between commensal microbes and the host immune system, highlighting the critical role of gut bacteria in maintaining immune homeostasis. We examine how modern lifestyle practices and environmental factors have disrupted co-evolved host-microbe interactions and discuss how changes in microbiome composition impact epithelial barrier function, responses to food allergens, and susceptibility to allergic diseases. Finally, we examine the potential of bioengineered microbiome-based therapies, and live biotherapeutic products, for reestablishing immune homeostasis to prevent or treat food allergies.

Microplastics promote methane emission in estuarine and coastal wetlands

Increasing microplastic (MP) pollution poses significant threats to estuarine and coastal ecosystems. However, the effects of MPs on the emission of methane (CH4), a potent greenhouse gas, within these ecosystems and the underlying regulatory mechanisms have not been elucidated. Here, a combination of 13C stable isotope-based method and molecular techniques was applied to investigate how conventional petroleum-based MPs [polyethylene (PE) and polyvinyl chloride (PVC)] and biodegradable MPs [polylactic acid (PLA) and polyadipate/butylene terephthalate (PBAT)] regulate CH4 production and consumption and thus affect CH4 emission dynamics in estuarine and coastal wetlands. Results indicated that both conventional and biodegradable MPs enhanced the emission of CH4 (P < 0.05), with the promoting effect being more significant for biodegradable MPs. However, the mechanisms by which conventional and biodegradable MPs promote CH4 emissions were different. Specifically, conventional MPs stimulated the emission of CH4 by inhibiting the processes of CH4 consumption, but had no significant effect on CH4 production rate. Nevertheless, biodegradable MPs promoted CH4 emissions via accelerating the activities the methanogens while inhibiting the oxidation of CH4, thus resulting in a higher degree of promoting effect on CH4 emissions than conventional MPs. Consistently, quantitative PCR further revealed a significant increase in the abundance of methyl-coenzyme M reductase gene (mcrA) of methanogens under the exposure of biodegradable MPs (P < 0.05), but not conventional MPs. Furthermore, the relative abundance of most genes involved in CH4 oxidation exhibited varying degrees of reduction after exposure to all types of MPs, based on metagenomics data. This study reveals the effects of MPs on CH4 emissions in estuarine and coastal ecosystems and their underlying mechanisms, highlighting that the emerging biodegradable MPs exhibited a greater impact than conventional MPs on promoting CH4 emissions in these globally important ecosystems, thereby accelerating global climate change.

Microbiota based personalized nutrition improves hyperglycaemia and hypertension parameters and reduces inflammation: a prospective, open label, controlled, randomized, comparative, proof of concept study

Background

Recent studies suggest that gut microbiota composition, abundance and diversity can influence many chronic diseases such as type 2 diabetes. Modulating gut microbiota through targeted nutrition can provide beneficial effects leading to the concept of personalized nutrition for health improvement. In this prospective clinical trial, we evaluated the impact of a microbiome-based targeted personalized diet on hyperglycaemic and hyperlipidaemic individuals. Specifically, BugSpeaks®-a microbiome profile test that profiles microbiota using next generation sequencing and provides personalized nutritional recommendation based on the individual microbiota profile was evaluated.

Methods

A total of 30 participants with type 2 diabetes and hyperlipidaemia were recruited for this study. The microbiome profile of the 15 participants (test arm) was evaluated using whole genome shotgun metagenomics and personalized nutritional recommendations based on their microbiota profile were provided. The remaining 15 participants (control arm) were provided with diabetic nutritional guidance for 3 months. Clinical and anthropometric parameters such as HbA1c, systolic/diastolic pressure, c-reactive protein levels and microbiota composition were measured and compared during the study.

Results

The test arm (microbiome-based nutrition) showed a statistically significant decrease in HbA1c level from 8.30 (95% confidence interval (CI), [7.74-8.85]) to 6.67 (95% CI [6.2-7.05]), p < 0.001 after 90 days. The test arm also showed a 5% decline in the systolic pressure whereas the control arm showed a 7% increase. Incidentally, a sub-cohort of the test arm of patients with >130 mm Hg systolic pressure showed a statistically significant decrease of systolic pressure by 14%. Interestingly, CRP level was also found to drop by 19.5%. Alpha diversity measures showed a significant increase in Shannon diversity measure (p < 0.05), after the microbiome-based personalized dietary intervention. The intervention led to a minimum two-fold (Log2 fold change increase in species like Phascolarctobacterium succinatutens, Bifidobacterium angulatum, and Levilactobacillus brevis which might have a beneficial role in the current context and a similar decrease in species like Alistipes finegoldii, and Sutterella faecalis which have been earlier shown to have some negative effects in the host. Overall, the study indicated a net positive impact of the microbiota based personalized dietary regime on the gut microbiome and correlated clinical parameters.

Gut microbiota-derived gamma-aminobutyric acid from metformin treatment reduces hepatic ischemia/reperfusion injury through inhibiting ferroptosis

Hepatic ischemia/reperfusion injury (HIRI) is a common and inevitable factor leading to poor prognosis in various liver diseases, making the outcomes of current treatments in clinic unsatisfactory. Metformin has been demonstrated to be beneficial to alleviate HIRI in recent studies, however, the underpinning mechanism remains unclear. In this study, we found metformin mitigates HIRI-induced ferroptosis through reshaped gut microbiota in mice, which was confirmed by the results of fecal microbiota transplantation treatment but showed the elimination of the beneficial effects when gut bacteria were depleted using antibiotics. Detailedly, through 16S rRNA and metagenomic sequencing, we identified that the metformin-reshaped microbiota was characterized by the increase of gamma-aminobutyric acid (GABA) producing bacteria. This increase was further confirmed by the elevation of GABA synthesis key enzymes, glutamic acid decarboxylase and putrescine aminotransferase, in gut microbes of metformin-treated mice and healthy volunteers. Furthermore, the benefit of GABA against HIRI-induced ferroptosis was demonstrated in GABA-treated mice. Collectively, our data indicate that metformin can mitigate HIRI-induced ferroptosis by reshaped gut microbiota, with GABA identified as a key metabolite.

The effect of in vitro simulated colonic pH gradients on microbial activity and metabolite production using common prebiotics as substrates

BACKGROUND

The interplay between gut microbiota (GM) and the metabolization of dietary components leading to the production of short-chain fatty acids (SCFAs) is affected by a range of factors including colonic pH and carbohydrate source. However, there is still only limited knowledge on how the GM activity and metabolite production in the gastrointestinal tract could be influenced by pH and the pH gradient increases along the colon.

RESULTS

Here we investigate the effect of pH gradients corresponding to levels typically found in the colon on GM composition and metabolite production using substrates inulin, lactose, galactooligosaccharides (GOS), and fructooligosaccharide (FOS) in an in vitro colon setup. We investigated 3 different pH regimes (low, 5.2 increasing to 6.4; medium, 5.6 increasing to 6.8 and high, 6.0 increasing to 7.2) for each fecal inoculum and found that colonic pH gradients significantly influenced in vitro simulated GM structure, but the influence of fecal donor and substrate was more pronounced. Low pH regimes strongly influenced GM with the decreased relative abundance of Bacteroides spp. and increased Bifidobacterium spp. Higher in vitro simulated colonic pH promoted the production of SCFAs in a donor- and substrate-dependent manner. The butyrate producer Butyricimonas was enriched at higher pH conditions, where also butyrate production was increased for inulin. The relative abundance of Phascolarctobacterium, Bacteroides, and Rikenellaceae also increased at higher colonic pH, which was accompanied by increased production of propionate with GOS and FOS as substrates.

CONCLUSIONS

Together, our results show that colonic substrates such as dietary fibres influence GM composition and metabolite production, not only by being selectively utilized by specific microbes, but also because of their SCFA production, which in turn also influences colonic pH and overall GM composition and activity. Our work provides details about the effect of the gradients of rising pH from the proximal to distal colon on fermenting dietary substrates in vitro and highlights the importance of considering pH in GM research.

Effects of dietary β-glucans on the productive performance, blood parameters, and intestinal microbiota of angelfish (Pterophyllum scalare) juveniles

Among the potential feed additives, β-glucans are known to positively affect the growth performance, blood parameters, and intestinal microbiota of fish, even the ornamental species. Therefore, the present study evaluated the effects of the dietary supplementation of different Saccharomyces cerevisiae β-glucans concentrations (0, 0.05, 0.1, and 0.2%) in juvenile angelfish (Pterophyllum scalare) over a 42-day period. Regarding growth performance, no effects were observed on most parameters. However, 0.2% β-glucans supplementation produced higher condition factor values, indicating a better nutritional status. Furthermore, β-glucans supplementation did not affect blood parameters. Regarding intestinal microbiota, β-glucans supplementation increased the abundance of the potentially beneficial bacterial genus Phascolarctobacterium. The high abundance of bacteria from the phylum Bacteroidetes, which can degrade β-glucans, may be attributed to the increased abundance of Phascolarctobacterium spp. In addition, 0.2% β-glucans supplementation produced more operational taxonomic units and higher Sobs (observed species richness), indicating effects on the overall bacterial community structure. These results demonstrate the potential application of β-glucans as a dietary supplement to improve the performance and modulate the intestinal microbiota of angelfish.

In vitro digestion and fecal fermentation of selenocompounds: impact on gut microbiota, antioxidant activity, and short-chain fatty acids

Selenium bioavailability is critically influenced by gut microbiota, yet the interaction dynamics with selenocompounds remain unexplored. Our study found that L-Selenomethionine (SeMet) and Se-(Methyl)seleno-L-cysteine (MeSeCys) maintained stability during in vitro gastrointestinal digestion. In contrast, Selenite and L-Selenocystine (SeCys2) were degraded by approximately 13% and 35%. Intriguingly, gut microflora transformed MeSeCys, SeCys2, and Selenite into SeMet. Moreover, when SeCys2 and Selenite incubated with gut microbiota, they produced red selenium nanoparticles with diameters ranging between 100 and 400 nm and boosted glutathione peroxidase activity. These changes were positively associated with an increased relative abundance of unclassified_g__Blautia (Family Lachnospiraceae), Erysipelotrichaceae_UCG-003 (Family Erysipelatoclostridiaceae), and uncultured_bacterium_g__Subdoligranulum (Family Ruminococcaceae). Our findings implied that differential microbial sensitivities to selenocompounds, potentially attributable to their distinct mechanisms governing selenium uptake, storage, utilization, and excretion.

High-throughput characterization of the effect of sodium chloride and potassium chloride on 31 lactic acid bacteria and their co-cultures

Salt (NaCl) is associated with a risk of hypertension and the development of coronary heart disease, so its consumption should be limited. However, salt plays a key role in the quality and safety of food by controlling undesirable microorganisms. Since studies have focused primarily on the effect of salts on the overall counts of the lactic acid bacteria (LAB) group, we have not yet understood how salt stress individually affects the strains and the interactions between them. In this study, we characterized the effect of sodium chloride (NaCl) and potassium chloride (KCl) on the growth and acidification of 31 LAB strains. In addition, we evaluated the effect of salts on a total of 93 random pairwise strain combinations. Strains and co-cultures were tested at 3% NaCl, 5% NaCl, and 3% KCl on solid medium using an automated approach and image analysis. The results showed that the growth of LAB was significantly reduced by up to 68% at 5% NaCl (p < 0.0001). For the co-cultures, a reduction of up to 57% was observed at 5% NaCl (p < 0.0001). However, acidification was less affected by salt stress, whether for monocultures or co-cultures. Furthermore, KCl had a lesser impact on both growth and acidification compared to NaCl. Indeed, some strains showed a significant increase in growth at 3% KCl, such as Lactococcus lactis subsp. lactis 74310 (23%, p = 0.01). More importantly, co-cultures appeared to be more resilient and had more varied responses to salt stress than the monocultures, as several cases of suppression of the significant effect of salts on acidification and growth were detected. Our results highlight that while salts can modulate microbial interactions, these latter can also attenuate the effect of salts on LAB.

Microbiota encoded fatty-acid metabolism expands tuft cells to protect tissues homeostasis during Clostridioides difficile infection in the large intestine

Metabolic byproducts of the intestinal microbiota are crucial in maintaining host immune tone and shaping inter-species ecological dynamics. Among these metabolites, succinate is a driver of tuft cell (TC) differentiation and consequent type 2 immunity-dependent protection against invading parasites in the small intestine. Succinate is also a growth enhancer of the nosocomial pathogen Clostridioides difficile in the large intestine. To date, no research has shown the role of succinate in modulating TC dynamics in the large intestine, or the relevance of this immune pathway to C. difficile pathophysiology. Here we reveal the existence of a three-way circuit between commensal microbes, C. difficile and host epithelial cells which centers around succinate. Through selective microbiota depletion experiments we demonstrate higher levels of type 2 cytokines leading to expansion of TCs in the colon. We then demonstrate the causal role of the microbiome in modulating colonic TC abundance and subsequent type 2 cytokine induction using rational supplementation experiments with fecal transplants and microbial consortia of succinate-producing bacteria. We show that administration of a succinate-deficient Bacteroides thetaiotaomicron knockout (Δfrd) significantly reduces the enhanced type 2 immunity in mono-colonized mice. Finally, we demonstrate that mice prophylactically administered with the consortium of succinate-producing bacteria show reduced C. difficile-induced morbidity and mortality compared to mice administered with heat-killed bacteria or the vehicle. This effect is reduced in a partial tuft cell knockout mouse, Pou2f3+/-, and nullified in the tuft cell knockout mouse, Pou2f3-/-, confirming that the observed protection occurs via the TC pathway. Succinate is an intermediary metabolite of the production of short-chain fatty acids, and its concentration often increases during dysbiosis. The first barrier to enteric pathogens alike is the intestinal epithelial barrier, and host maintenance and strengthening of barrier integrity is vital to homeostasis. Considering our data, we propose that activation of TC by the microbiota-produced succinate in the colon is a mechanism evolved by the host to counterbalance microbiome-derived cues that facilitate invasion by intestinal pathogens.

Human gut microbiota and their production of endocannabinoid-like mediators are directly affected by a dietary oil

Dietary omega-3 polyunsaturated fatty acids (n-3 PUFAs) and the gut microbiome affect each other. We investigated the impact of supplementation with Buglossoides arvensis oil (BO), rich in stearidonic acid (SDA), on the human gut microbiome. Employing the Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME), we simulated the ileal and ascending colon microbiomes of four donors. Our results reveal two distinct microbiota clusters influenced by BO, exhibiting shared and contrasting shifts. Notably, Bacteroides and Clostridia abundance underwent similar changes in both clusters, accompanied by increased propionate production in the colon. However, in the ileum, cluster 2 displayed a higher metabolic activity in terms of BO-induced propionate levels. Accordingly, a triad of bacterial members involved in propionate production through the succinate pathway, namely Bacteroides, Parabacteroides, and Phascolarctobacterium, was identified particularly in this cluster, which also showed a surge of second-generation probiotics, such as Akkermansia, in the colon. Finally, we describe for the first time the capability of gut bacteria to produce N-acyl-ethanolamines, and particularly the SDA-derived N-stearidonoyl-ethanolamine, following BO supplementation, which also stimulated the production of another bioactive endocannabinoid-like molecule, commendamide, in both cases with variations across individuals. Spearman correlations enabled the identification of bacterial genera potentially involved in endocannabinoid-like molecule production, such as, in agreement with previous reports, Bacteroides in the case of commendamide. This study suggests that the potential health benefits on the human microbiome of certain dietary oils may be amenable to stratified nutrition strategies and extend beyond n-3 PUFAs to include microbiota-derived endocannabinoid-like mediators.

Effects of Prebiotic Yeast Mannan on Gut Health and Sleep Quality in Healthy Adults: A Randomized, Double-Blind, Placebo-Controlled Study

Human gut health is closely related to sleep. We aimed to evaluate the efficacy of yeast mannan (YM) in improving bowel habits and sleep quality, along with metabolomics in fecal samples. A total of 40 healthy adults (age range, 22-64 years) with discomfort in defecation were enrolled and randomly allocated to receive either YM (n = 20; 1.1 g/day) or placebo (n = 20) for four weeks. Participants recorded their defecation habits throughout the test periods. Sleep electroencephalogram (EEG) recording using an EEG device and fecal sampling were performed pre- and post-treatment. The YM group significantly increased defecation frequency and stool volumes compared to the placebo group. After 4 weeks of treatment, the non-REM sleep stage 3 (N3) duration in the YM group was significantly higher than that in the placebo group. YM ingestion significantly lengthened total time in bed (TIB) and significantly shortened N3 latency compared to placebo intake during the trial. The metabolomics analysis found a total of 20 metabolite differences between the YM and placebo groups. As a result of stepwise linear regression, changes in fecal propionate and gamma-aminobutyric acid (GABA) levels were identified as the primary factors explaining changes in TIB and N3 latency, respectively. Our findings suggest that the prebiotic YM could be beneficial to gut health and sleep quality.

Rumen and fecal microbiomes are related to diet and production traits in Bos indicus beef cattle

Background

Ruminants harbor a complex microbial community within their gastrointestinal tract, which plays major roles in their health and physiology. Brazil is one of the largest producers of beef in the world and more than 90% of the beef cattle herds are composed of pure and crossbred Nelore (Bos indicus). Despite its importance to the Brazilian economy and human feeding, few studies have characterized the Nelore microbiome. Therefore, using shotgun metagenomics, we investigated the impact of diet on the composition and functionality of the Nelore microbiome, and explored the associations between specific microbial taxa and their functionality with feed efficiency and methane emission.

Results

The ruminal microbiome exhibited significantly higher microbial diversity, distinctive taxonomic profile and variations in microbial functionality compared to the fecal microbiome, highlighting the distinct contributions of the microbiomes of these environments. Animals subjected to different dietary treatments exhibited significant differences in their microbiomes' archaeal diversity and in the abundance of 89 genera, as well as in the functions associated with the metabolism of components of each diet. Moreover, depending on the diet, feed-efficient animals and low methane emitters displayed higher microbial diversity in their fecal microbiome. Multiple genera were associated with an increase or decrease of the phenotypes. Upon analyzing the functions attributed to these taxa, we observed significant differences on the ruminal taxa associated with feed efficient and inefficient cattle. The ruminal taxa that characterized feed efficient cattle stood out for having significantly more functions related to carbohydrate metabolism, such as monosaccharides, di-/oligosaccharides and amino acids. The taxa associated with methane emission had functions associated with methanogenesis and the production of substrates that may influence methane production, such as hydrogen and formate.

Conclusion

Our findings highlight the significant role of diet in shaping Nelore microbiomes and how its composition and functionality may affect production traits such as feed efficiency and methane emission. These insights provide valuable support for the implementation of novel feeding and biotechnological strategies.

In vitro faecal fermentation of Tritordeum breads and its effect on the human gut health

Spontaneous fermentation of Tritordeum flour enhances the nutritional potential of this hybrid cereal. However, the effect of consumption of Tritordeum sourdough bread (SDB) on gut health remains to be elucidated. This study investigated the effect of in vitro digestion and faecal fermentation of SDB compared to that of traditional baker's yeast (BYB) Tritordeum bread. After 24-h anaerobic faecal fermentation, both SDB and BYB (1% w/v) induced an increase in the relative abundances of Bifidobacterium, Megasphaera, Mitsuokella, and Phascolarctobacterium genera compared to baseline, while concentrations of acetate and butyrate were significantly higher at 24 h for SDB compared to those for BYB. Integrity of intestinal epithelium, as assessed through in vitro trans-epithelial electrical resistance (TEER) assay, was slightly increased after incubation with SDB fermentation supernatants, but not after incubation with BYB fermentation supernatants. The SDB stimulated in vitro mucosal immune response by inducing early secretion of inflammatory cytokines, IL-6 and TNF-α, followed by downregulation of the inflammatory trigger through induction of anti-inflammatory IL-10 expression. Overall, our findings suggest that Tritordeum sourdough can modulate gut microbiota fermentation activity and positively impact the gut health.

Fecal Microbiota and Associated Volatile Organic Compounds Distinguishing No-Adenoma from High-Risk Colon Adenoma Adults

Microbiota and the metabolites they produce within the large intestine interact with the host epithelia under the influence of a range of host-derived metabolic, immune, and homeostatic factors. This complex host-microbe interaction affects intestinal tumorigenesis, but established microbial or metabolite profiles predicting colorectal cancer (CRC) risk are missing. Here, we aimed to identify fecal bacteria, volatile organic compounds (VOC), and their associations that distinguish healthy (non-adenoma, NA) from CRC prone (high-risk adenoma, HRA) individuals. Analyzing fecal samples obtained from 117 participants ≥15 days past routine colonoscopy, we highlight the higher abundance of Proteobacteria and Parabacteroides distasonis, and the lower abundance of Lachnospiraceae species, Roseburia faecis, Blautia luti, Fusicatenibacter saccharivorans, Eubacterium rectale, and Phascolarctobacterium faecium in the samples of HRA individuals. Volatolomic analysis of samples from 28 participants revealed a higher concentration of five compounds in the feces of HRA individuals, isobutyric acid, methyl butyrate, methyl propionate, 2-hexanone, and 2-pentanone. We used binomial logistic regression modeling, revealing 68 and 96 fecal bacteria-VOC associations at the family and genus level, respectively, that distinguish NA from HRA endpoints. For example, isobutyric acid associations with Lachnospiraceae incertae sedis and Bacteroides genera exhibit positive and negative regression lines for NA and HRA endpoints, respectively. However, the same chemical associates with Coprococcus and Colinsella genera exhibit the reverse regression line trends. Thus, fecal microbiota and VOC profiles and their associations in NA versus HRA individuals indicate the significance of multiple levels of analysis towards the identification of testable CRC risk biomarkers.

Systematic exploration of transcriptional responses of interspecies interaction between Karenia mikimotoi and Prorocentrum shikokuense

Karenia mikimotoi and Prorocentrum shikokuense (also identified as P. donghaiense Lu and P. obtusidens Schiller) are two important harmful algal species which often form blooms in the coasts of China. Studies have shown that the allelopathy of K. mikimotoi and P. shikokuense plays an important role in inter-algal competition, though the underlying mechanisms remain largely unclear. Here, we observed reciprocal inhibitory effects between K. mikimotoi and P. shikokuense under co-cultures. Based on the reference sequences, we isolated RNA sequencing reads of K. mikimotoi and P. shikokuense from co-culture metatranscriptome, respectively. We found the genes involved in photosynthesis, carbon fixation, energy metabolism, nutrients absorption and assimilation were significantly up-regulated in K. mikimotoi after co-cultured with P. shikokuense. However, genes involved in DNA replication and cell cycle were significantly down-regulated. These results suggested that co-culture with P. shikokuense stimulated cell metabolism and nutrients competition activity of K. mikimotoi, and inhibited cell cycle. In contrast, genes involved in energy metabolism, cell cycle and nutrients uptake and assimilation were dramatically down-regulated in P. shikokuense under co-culture with K. mikimotoi, indicating that K. mikimotoi could highly affect the cellular activity of P. shikokuense. In addition, the expression of PLA2G12 (Group XII secretory phospholipase A2) that can catalyze the accumulation of linoleic acid or linolenic acid, and nitrate reductase that may be involved in nitric oxide production were significantly increased in K. mikimotoi, suggesting that PLA2G12 and nitrate reductase may play important roles in the allelopathy of K. mikimotoi. Our findings shed new light on the interspecies competition between K. mikimotoi and P. shikokuense, and provide a novel strategy for studying interspecific competition in complex systems.

Effects of Four Extraction Methods on Structure and In Vitro Fermentation Characteristics of Soluble Dietary Fiber from Rape Bee Pollen

In this study, soluble dietary fibers (SDFs) were extracted from rape bee pollen using four methods including acid extraction (AC), alkali extraction (AL), cellulase extraction (CL) and complex enzyme extraction (CE). The effects of different extraction methods on the structure of SDFs and in vitro fermentation characteristics were further investigated. The results showed that the four extraction methods significantly affected the monosaccharide composition molar ratio, molecular weight, surface microstructure and phenolic compounds content, but showed little effect on the typical functional groups and crystal structure. In addition, all SDFs decreased the Firmicutes/Bacteroidota ratio, promoted the growth of beneficial bacteria such as Bacteroides, Parabacteroides and Phascolarctobacterium, inhibited the growth of pathogenic bacteria such as Escherichia-Shigella, and increased the total short-chain fatty acids (SCFAs) concentrations by 1.63-2.45 times, suggesting that the bee pollen SDFs had a positive regulation on gut microbiota. Notably, the SDF obtained by CE exhibited the largest molecular weight, a relatively loose structure, higher extraction yield and phenolic compounds content and the highest SCFA concentration. Overall, our results indicated that CE was an appropriate extraction method of high-quality bee pollen SDF.

Dietary Berberine and Ellagic Acid Supplementation Improve Growth Performance and Intestinal Damage by Regulating the Structural Function of Gut Microbiota and SCFAs in Weaned Piglets

Early weaning is an effective method for improving the utilization rate of sows in intensive pig farms. However, weaning stress induces diarrhea and intestinal damage in piglets. Berberine (BBR) is known for its anti-diarrhea properties and ellagic acid (EA) is known for its antioxidant properties, however, whether their combination improves diarrhea and intestinal damage in piglets has not been studied, and the mechanism remains unclear. To explore the combined effects in this experiment, a total of 63 weaned piglets (Landrace × Yorkshire) were divided into three groups at 21 days. Piglets in the Ctrl group were treated with a basal diet and 2 mL saline orally, while those in the BE group were treated with a basal diet supplemented with 10 mg/kg (BW) BBR, 10 mg/kg (BW) EA, and 2 mL saline orally. Piglets in the FBE group were treated with a basal diet and 2 mL fecal microbiota suspension from the BE group orally, respectively, for 14 days. Compared with the Ctrl group, dietary supplementation with BE improved growth performance by increasing the average daily gain and average daily food intake and reducing the fecal score in weaned piglets. Dietary supplementation with BE also improved intestinal morphology and cell apoptosis by increasing the ratio of villus height to crypt depth and decreasing the average optical density of apoptotic cells; meanwhile, improvements also involved attenuating oxidative stress and intestinal barrier dysfunction by increasing the total antioxidant capacity, glutathione, and catalase, and upregulating the mRNA expressions of Occludin, Claudin-1, and ZO-1. Interestingly, the oral administration of a fecal microbiota suspension to piglets fed BE had similar effects to those of the BE group. According to 16S rDNA sequencing analysis, dietary supplementation with BE altered the composition of the microbiota, including firmicutes, bacteroidetes, lactobacillus, phascolarctobacterium, and parabacteroides, and increased the metabolites of propionate and butyrate. In addition, Spearman analysis revealed that improvements in growth performance and intestinal damage were significantly correlated with differential bacteria and short-chain fatty acids (SCFAs). In brief, dietary supplementation with BE improved the growth performance and intestinal damage by altering the gut microbiota composition and SCFAs in weaned piglets.

Double emulsions as a high-throughput enrichment and isolation platform for slower-growing microbes

Our understanding of in situ microbial physiology is primarily based on physiological characterization of fast-growing and readily-isolatable microbes. Microbial enrichments to obtain novel isolates with slower growth rates or physiologies adapted to low nutrient environments are plagued by intrinsic biases for fastest-growing species when using standard laboratory isolation protocols. New cultivation tools to minimize these biases and enrich for less well-studied taxa are needed. In this study, we developed a high-throughput bacterial enrichment platform based on single cell encapsulation and growth within double emulsions (GrowMiDE). We showed that GrowMiDE can cultivate many different microorganisms and enrich for underrepresented taxa that are never observed in traditional batch enrichments. For example, preventing dominance of the enrichment by fast-growing microbes due to nutrient privatization within the double emulsion droplets allowed cultivation of slower-growing Negativicutes and Methanobacteria from stool samples in rich media enrichment cultures. In competition experiments between growth rate and growth yield specialist strains, GrowMiDE enrichments prevented competition for shared nutrient pools and enriched for slower-growing but more efficient strains. Finally, we demonstrated the compatibility of GrowMiDE with commercial fluorescence-activated cell sorting (FACS) to obtain isolates from GrowMiDE enrichments. Together, GrowMiDE + DE-FACS is a promising new high-throughput enrichment platform that can be easily applied to diverse microbial enrichments or screens.

Intestinal Damages by F18+Escherichia coli and Its Amelioration with an Antibacterial Bacitracin Fed to Nursery Pigs

This study investigated intestinal oxidative damage caused by F18⁺Escherichia coli and its amelioration with antibacterial bacitracin fed to nursery pigs. Thirty-six weaned pigs (6.31 ± 0.08 kg BW) were allotted in a randomized complete block design. Treatments were: NC, not challenged/not treated; PC, challenged (F18⁺E. coli at 5.2 × 10⁹ CFU)/not treated; AGP challenged (F18⁺E. coli at 5.2 × 10⁹ CFU)/treated with bacitracin (30 g/t). Overall, PC reduced (p < 0.05) average daily gain (ADG), gain to feed ratio (G:F), villus height, and villus height to crypt depth ratio (VH:CD), whereas AGP increased (p < 0.05) ADG, and G:F. PC increased (p < 0.05) fecal score, F18⁺E. coli in feces, and protein carbonyl in jejunal mucosa. AGP reduced (p < 0.05) fecal score and F18⁺E. coli in jejunal mucosa. PC reduced (p < 0.05) Prevotella stercorea populations in jejunal mucosa, whereas AGP increased (p < 0.05) Phascolarctobacterium succinatutens and reduced (p < 0.05) Mitsuokella jalaludinii populations in feces. Collectively, F18⁺E. coli challenge increased fecal score and disrupted the microbiota composition, harming intestinal health by increasing oxidative stress, and damaging the intestinal epithelium, ultimately impairing growth performance. Dietary bacitracin reduced reduced F18⁺E. coli populations and the oxidative damages they cause, thereby improving intestinal health and the growth performance of nursery pigs.

Intravaginal injection of Lactobacillus johnsonii may modulates oviductal microbiota and mucosal barrier function of laying hens

The avian oviduct connects to the gastrointestinal tract through cloaca, where it is exposed to pathogenic bacteria from intestinal contents. Therefore, improvement of mucosal barrier function in the oviduct is important for safe poultry production. Lactic acid bacteria are known to contribute to strengthening the mucosal barrier function in the intestinal tract, and a similar effect is expected in the oviduct mucosa of chickens. This study aimed to clarify the effects of vaginal administration of lactic acid bacteria on the mucosal barrier function of the oviduct. White Leghorn laying hens (500-days old) were intravaginally administered 1 mL of Lactobacillus johnsonii suspension (1 × 10⁵ and 1 × 10⁸ cfu/mL: low concentration of Lactobacillus (LL) and high concentration of Lactobacillus (HL) groups, respectively) or without bacteria (control: C group) for 7 d (n = 6). The oviductal magnum, uterus, and vagina were collected for histological observations and mucosal barrier function-related gene expression analysis. Amplicon sequence analysis of oviductal mucus bacteria was also performed. Eggs were collected during the experimental period and their weight was measured. Vaginally administering L. johnsonii for 7 d caused 1) an increase in α-diversity of vaginal mucosa microbiota with an increase in the abundance ratio of beneficial bacteria and a decrease in pathogenic bacteria, 2) enhanced claudin (CLA) 1 and 3 gene expression in the magnum and vaginal mucosa, and 3) a decrease in avian β-defensin (AvBD) 10, 11, and 12 gene expression in the magnum, uterus, and vaginal mucosa. These results suggest that transvaginal administration of L. johnsonii contributes to protection against infection in the oviduct by improving the microflora of the oviductal mucosa and strengthening the mechanical barrier function of the tight junctions. In contrast, transvaginal administration of lactic acid bacteria does not enhance the production of AvBD10, 11, and 12 in the oviduct.

Alteration of gut microbiota in wild-borne long-tailed macaques after 1-year being housed in hygienic captivity

The wild-born long-tailed macaques (Macaca fascicularis) were recently recruited and used as breeders for the National Primate Research Center of Thailand, Chulalongkorn University (NPRCT-CU), and changes in their in-depth gut microbiota profiles were investigated. The Oxford Nanopore Technology (ONT) was used to explore full-length 16S rDNA sequences of gut microbiota in animals once captured in their natural habitat and 1-year following translocation and housing in a hygienic environment at NPRCT-CU. Our findings show that the gut microbiota of macaques after 1 year of hygienic housing and programmed diets feeding was altered and reshaped. The prevalent gut bacteria such as Prevotella copri and Faecalibacterium prausnitzii were enriched after translocation, causing the lower alpha diversity. The correlation analysis revealed that Prevotella copri, Phascolarctobacterium succinatutens, and Prevotella stercorea, showed a positive correlation with each other. Significantly enriched pathways in the macaques after translocation included biosynthesis of essential amino acids, fatty acids, polyamine and butanoate. The effects of microbiota change could help macaques to harvest the energy from programmed diets and adapt their gut metabolism. The novel probiotics and microbiota engineering approach could be further developed based on the current findings and should be helpful for captive animal health care management.

Temporal dynamics of the cecal and litter microbiome of chickens raised in two separate broiler houses

In this study, we investigated the dynamics of the ceca and litter microbiome of chickens from post-hatch through pre-harvest. To achieve this, six hundred one-day old Cobb 500 broiler chicks were raised on floor pens for 49 days in two separate houses. We performed short-read and full-length sequencing of the bacterial 16S rRNA gene present in the meconium and in cecal and litter samples collected over the duration of the study. In addition, we determined the antimicrobial resistance (AMR) phenotype of Escherichia coli and Enterococcus spp. isolated from the meconium and the ceca of 49-day old chickens. We monitored the relative humidity, temperature, and ammonia in each house daily and the pH and moisture of litter samples weekly. The overall microbial community structure of the ceca and litter consistently changed throughout the course of the grow-out and correlated with some of the environmental parameters measured (p < 0.05). We found that the ceca and litter microbiome were similar in the two houses at the beginning of the experiment, but over time, the microbial community separated and differed between the houses. When we compared the environmental parameters in the two houses, we found no significant differences in the first half of the growth cycle (day 0-21), but morning temperature, morning humidity, and ammonia significantly differed (p < 0.05) between the two houses from day 22-49. Lastly, the prevalence of AMR in cecal E. coli isolates differed from meconium isolates (p < 0.001), while the AMR phenotype of cecal Enterococcus isolates differed between houses (p < 0.05).

Succinate metabolism and its regulation of host-microbe interactions

Succinate is a circulating metabolite, and the relationship between abnormal changes in the physiological concentration of succinate and inflammatory diseases caused by the overreaction of certain immune cells has become a research focus. Recent investigations have shown that succinate produced by the gut microbiota has the potential to regulate host homeostasis and treat diseases such as inflammation. Gut microbes are important for maintaining intestinal homeostasis. Microbial metabolites serve as nutrients in energy metabolism, and act as signal molecules that stimulate host cell and organ function and affect the structural balance between symbiotic gut microorganisms. This review focuses on succinate as a metabolite of both host cells and gut microbes and its involvement in regulating the gut - immune tissue axis by activating intestinal mucosal cells, including macrophages, dendritic cells, and intestinal epithelial cells. We also examined its role as the mediator of microbiota - host crosstalk and its potential function in regulating intestinal microbiota homeostasis. This review explores feasible ways to moderate succinate levels and provides new insights into succinate as a potential target for microbial therapeutics for humans.

Healthy adult gut microbiota sustains its own vitamin B12 requirement in an in vitro batch fermentation model

Vitamin B12 (cobalamin) is present in the human lower gastrointestinal tract either coming from the unabsorbed dietary fraction or from in situ production of the gut microbiota. However, it is unclear whether the gut microbial communities need exogenous B12 for growth and metabolism, or whether B12 in low and high levels could affect gut community composition and metabolite production. Here, we investigated in vitro B12 production of human fecal microbiota and the effects of different levels of B12 (as cyanocobalamin) on composition and activity. Eight fecal communities from healthy human adults distributed over three enterotypes, dominated by Firmicutes (n = 5), Bacteroides (n = 1) or Prevotella (n = 2) were used to perform batch fermentations in Macfarlane medium supplemented with low B12 medium (Control, 5 ng/ml, within the tested fecal range), no B12 addition (NB12), and high B12 addition (ExtraB12, 2500 ng/ml). The microbiota community composition (qPCR, 16S rRNA metabarcoding), metabolic activity (HPLC-RI), and B12 levels (UHPLC-DAD) were measured after 24 h incubation at 37°C under strict anaerobic conditions. All fecal microbial communities produced B12 in the NB12 condition after 24 h, in the range from 152 ± 4 to 564 ± 25 ng/ml. None of the B12 treatments had an impact on total bacterial growth, community richness, diversity and total metabolite production, compared to the low B12 control. However, a significant increase of propionate was measured in ExtraB12 compared to NB12. Most taxonomic and metabolite changes compared to control incubations were donor-dependent, implying donor-microbiota-specific changes upon B12 treatments. Our in vitro data suggest that healthy human adult gut microbial communities have the capacity to produce B12 at levels fulfilling their own requirements, independently of the initial B12 content tested in the donor's feces. Further, supplementation of exogenous dietary B12 may have limited impact on the healthy human gut microbial community composition and function.

Bacillus amyloliquefaciens 40 regulates piglet performance, antioxidant capacity, immune status and gut microbiota

Probiotics can improve animal growth performance and intestinal health. Bacillus species, Lactobacillus species, Bifidobacterium species, yeast etc. are the common types of probiotics. However, understanding the effects of probiotics on the immune status and gut microbiota of weaning piglets and how the probiotics exert their impact are still limited. This study aimed to investigate the effects of Bacillus amyloliquefaciens 40 (BA40) on the performance, immune status and gut microbiota of piglets. A total of 12 litters of newborn piglets were randomly divided into 3 groups. Piglets in control group were orally dosed with phosphate buffered saline; BA40 group and probiotics group were orally gavaged with resuspension BA40 and a probiotics product, respectively. The results showed that BA40 treatment significantly decreased (P < 0.05) the diarrhea incidence (from d 5 to 40), diamine oxidase, D-lactate, interleukin (IL)-1β and interferon-γ concentrations compared with control group and probiotics group. Meanwhile BA40 dramatically increased the total antioxidant capacity, IL-10 and secretory immunoglobulin-A concentrations in contrast to control group. For the microbial composition, BA40 modulated the microbiota by improving the abundance of Bacteroides, Phascolarctobacterium (producing short-chain fatty acids) and Desulfovibrio and reducing the proliferation of pathogens (Streptococcus, Tyzzerella, Vellionella and paraeggerthella). Meanwhile, a metabolic function prediction explained that carbohydrate metabolism and amino acid metabolism enriched in BA40 group in contrast to control group and probiotics group. For correlation analysis, the results demonstrated that BA40-enriched Phascolarctobacterium and Desulfovibrio provide insights into strategies for elevating the health status and performance of weaned piglets. Altogether, BA40 exerted stronger ability in decreasing diarrhea incidence and improved antioxidant activity, gut barrier function and immune status of piglets than the other treatments. Our study provided the experimental and theoretical basis for the application of BA40 in pig production.

Central and peripheral regulations mediated by short-chain fatty acids on energy homeostasis

The human gut microbiota influences obesity, insulin resistance, and the subsequent development of type 2 diabetes (T2D). The gut microbiota digests and ferments nutrients resulting in the production of short-chain fatty acids (SCFAs), which generate various beneficial metabolic effects on energy and glucose homeostasis. However, their roles in the central nervous system (CNS)-mediated outputs on the metabolism have only been minimally studied. Here, we explore what is known and future directions that may be worth exploring in this emerging area. Specifically, we searched studies or data in English by using PubMed, Google Scholar, and the Human Metabolome Database. Studies were filtered by time from 1978 to March 2022. As a result, 195 studies, 53 reviews, 1 website, and 1 book were included. One hundred and sixty-five of 195 studies describe the production and metabolism of SCFAs or the effects of SCFAs on energy homeostasis, glucose balance, and mental diseases through the gut-brain axis or directly by a central pathway. Thirty of 195 studies show that inappropriate metabolism and excessive of SCFAs are metabolically detrimental. Most studies suggest that SCFAs exert beneficial metabolic effects by acting as the energy substrate in the TCA cycle, regulating the hormones related to satiety regulation and insulin secretion, and modulating immune cells and microglia. These functions have been linked with AMPK signaling, GPCRs-dependent pathways, and inhibition of histone deacetylases (HDACs). However, the studies focusing on the central effects of SCFAs are still limited. The mechanisms by which central SCFAs regulate appetite, energy expenditure, and blood glucose during different physiological conditions warrant further investigation.

Growth of succinate consumer Dialister hominis is supported by Bacteroides thetaiotaomicron

This study revealed an interaction between the gut commensal bacterium Bacteroides thetaiotaomicron JCM 5827^T and asaccharolytic bacterium Dialister hominis JCM 33369^T, which uses succinate instead of carbohydrates for growth. D. hominis usually forms extremely small colonies on Brucella blood agar plates. However, when co-cultured with B. thetaiotaomicron, D. hominis grew noticeably and formed larger colonies than those in the single culture, especially near B. thetaiotaomicron colonies. Although D. hominis barely grew in Gifu anaerobic medium broth, adding 1% succinate improved its growth. In the mixed culture, the succinate produced by B. thetaiotaomicron was mostly converted to propionate. This result was consistent with the single culture of D. hominis in the succinate-containing broth and our previous report on Phascolarctobacterium faecium, a succinate-utilizing gut bacterium. Our series of studies suggests that syntrophy within the human gut microbiota occurs via succinate.

Role of Gut Microbiome in Autism Spectrum Disorder and Its Therapeutic Regulation

Autism spectrum disorder (ASD) is a neurological disorder that affects normal brain development. The recent finding of the microbiota-gut-brain axis indicates the bidirectional connection between our gut and brain, demonstrating that gut microbiota can influence many neurological disorders such as autism. Most autistic patients suffer from gastrointestinal (GI) symptoms. Many studies have shown that early colonization, mode of delivery, and antibiotic usage significantly affect the gut microbiome and the onset of autism. Microbial fermentation of plant-based fiber can produce different types of short-chain fatty acid (SCFA) that may have a beneficial or detrimental effect on the gut and neurological development of autistic patients. Several comprehensive studies of the gut microbiome and microbiota-gut-brain axis help to understand the mechanism that leads to the onset of neurological disorders and find possible treatments for autism. This review integrates the findings of recent years on the gut microbiota and ASD association, mainly focusing on the characterization of specific microbiota that leads to ASD and addressing potential therapeutic interventions to restore a healthy balance of gut microbiome composition that can treat autism-associated symptoms.

Encapsulins

Subcellular compartmentalization is a defining feature of all cells. In prokaryotes, compartmentalization is generally achieved via protein-based strategies. The two main classes of microbial protein compartments are bacterial microcompartments and encapsulin nanocompartments. Encapsulins self-assemble into proteinaceous shells with diameters between 24 and 42 nm and are defined by the viral HK97-fold of their shell protein. Encapsulins have the ability to encapsulate dedicated cargo proteins, including ferritin-like proteins, peroxidases, and desulfurases. Encapsulation is mediated by targeting sequences present in all cargo proteins. Encapsulins are found in many bacterial and archaeal phyla and have been suggested to play roles in iron storage, stress resistance, sulfur metabolism, and natural product biosynthesis. Phylogenetic analyses indicate that they share a common ancestor with viral capsid proteins. Many pathogens encode encapsulins, and recent evidence suggests that they may contribute toward pathogenicity. The existing information on encapsulin structure, biochemistry, biological function, and biomedical relevance is reviewed here.

Evaluation of the Effects of a Short Supplementation With Tannins on the Gut Microbiota of Healthy Subjects

Western diet, high in fats and sugars and low in greens, contributes to dysbiosis of the gut microbiota, which can lead to a variety of chronic diseases related with inflammation. Supplementation with bioactive compounds can help to maintain a healthy eubiotic state. Thus, we performed a 4-weeks nutritional intervention on healthy volunteers to investigate whether a blend of natural tannin extracts could induce healthy changes in the microbial intestinal ecosystem. Changes in the composition and functionality of the microbiota could be observed from the first two weeks onward. 16S rRNA amplicon next-generation sequencing (NGS) revealed a significant increase in microbial diversity at the end of the intervention, as well as trends toward increases in the relative abundances of several beneficial taxa, such as Ruminococcus bicirculans, Faecalibacterium prausnitzii, Lachnospiraceae UCG 010, Lachnospiraceae NK4A136, Bacteroides thetaiotaomicron and B. uniformis. Remarkably, some of the identified taxa were also identified as responsible for an increase in the production of short-chain fatty acids (SCFAs), microbial metabolites that contribute to the modulation of the immune system and have various other anti-inflammatory functions in the gut. Taken together, these results suggest that the tannin supplementation could exert a prebiotic effect by selectively stimulating the growth and the activity of bacteria that are advantageous for the host.

Fecal microbiota transplantation is safe and tolerable in patients with multiple sclerosis: A pilot randomized controlled trial

Background

Patients with MS have an altered gut microbiota compared to healthy individuals, as well as elevated small intestinal permeability, which may be contributing to the development and progression of the disease.

Objective

We sought to investigate if fecal microbiota transplantation was safe and tolerable in MS patients and if it could improve abnormal intestinal permeability.

Methods

Nine patients with MS were recruited and provided monthly FMTs for up to six months. The primary outcome investigated was change in peripheral blood cytokine concentrations. The secondary outcomes were gut microbiota composition, intestinal permeability, and safety (assessed with EDSS and MRI).

Results

The study was terminated early and was subsequently underpowered to assess whether peripheral blood cytokines were altered following FMTs. FMTs were safe in this group of patients. Two of five patients had elevated small intestinal permeability at baseline that improved to normal values following FMTs. Significant, donor-specific, beneficial alterations to the MS patient gut microbiota were observed following FMT.

Conclusion

FMT was safe and tolerable in this cohort of RRMS patients, may improve elevated small intestinal permeability, and has the potential to enrich for an MS-protective microbiota. Further studies with longer follow-up and larger sample sizes are required to determine if FMT is a suitable therapy for MS.

Effectiveness of Multistrain Probiotic Formulation on Common Infectious Disease Symptoms and Gut Microbiota Modulation in Flu-Vaccinated Healthy Elderly Subjects

The decline of the immune system with aging leads elderly people to be more susceptible to infections, posing high risk for their health. Vaccination is thus important to cope with this risk, even though not always effective. As a strategy to improve protection, adjuvants are used in concomitance with vaccines, however, occasionally producing important side effects. The use of probiotics has been proposed as an alternative to adjuvants due to their efficacy in reducing the risk of common infections through the interactions with the immune system and the gut microbiota. A placebo-controlled, randomized, double-blind, clinical trial was carried out on fifty elderly subjects, vaccinated for influenza, to determine the efficacy of a probiotic mixture in reducing common infection symptoms. The incidence of symptoms was evaluated after 28 days of probiotic intake (namely, T28) and after further 28 days of follow-up (namely, T56). The number of subjects, as well as the number of days with symptoms, was remarkably reduced at T28, and even more at T56 in the probiotic group. Furthermore, the influence of probiotics on immunological parameters was investigated, showing a significant positive improvement of total antioxidant capacity and β-defensin2 levels. Finally, faecal samples collected from participants were used to assess variations in the gut microbiota composition during the study, showing that probiotic intake enhanced the presence of genera related to a healthy status. Therefore, the collected results suggested that the treatment with the selected probiotic mixture could help in reducing common infectious disease symptom incidence through the stimulation of the immune system, improving vaccine efficacy, and modulating the composition of the resident gut microbiota by enhancing beneficial genera.

Leveraging Experimental Strategies to Capture Different Dimensions of Microbial Interactions

Microorganisms are a fundamental part of virtually every ecosystem on earth. Understanding how collectively they interact, assemble, and function as communities has become a prevalent topic both in fundamental and applied research. Owing to multiple advances in technology, answering questions at the microbial system or network level is now within our grasp. To map and characterize microbial interaction networks, numerous computational approaches have been developed; however, experimentally validating microbial interactions is no trivial task. Microbial interactions are context-dependent, and their complex nature can result in an array of outcomes, not only in terms of fitness or growth, but also in other relevant functions and phenotypes. Thus, approaches to experimentally capture microbial interactions involve a combination of culture methods and phenotypic or functional characterization methods. Here, through our perspective of food microbiologists, we highlight the breadth of innovative and promising experimental strategies for their potential to capture the different dimensions of microbial interactions and their high-throughput application to answer the question; are microbial interaction patterns or network architecture similar along different contextual scales? We further discuss the experimental approaches used to build various types of networks and study their architecture in the context of cell biology and how they translate at the level of microbial ecosystem.

Effects of novel flavonoid-enriched yogurt on the diversity of intestinal microbiota in mice

Soy isoflavone glycoside cannot be effectively absorbed by the human intestinal tract, but probiotics with related hydrolases can transform it into aglycone to promote its absorption. In this study, a novel flavonoid-enriched yogurt was developed using an isolated β-glucosidase-producing strain (Lactiplantibacillus plantarum GY). The flavonoid aglycone-enhanced yogurt was fed to ICR mice for 21 days, and its effects were observed. The yogurt can affect the gut microbial diversity of mice, especially increasing the abundance of Parasutterella, the Bacteroidales S24-7 group, and Phascolarctobacterium in the intestinal tract of mice. Meanwhile, the ratio of Bacteroidetes/Firmicutes in the intestinal tract of mice fed with the flavonoid aglycone-enriched yogurt increased. The difference in the content of butyric acid between the L-GY + IS and the control groups was significant (P < 0.05). Therefore, milk fermentation with β-glucosidase-producing strains is a promising approach for developing flavonoid glycoside-enriched yogurt products.

Structural characterization and in vitro fermentation by rat intestinal microbiota of a polysaccharide from Porphyra haitanensis

A sulfated polysaccharide (PHP1) produced by the marine red alga Porphyra haitanensis was structurally characterized, and its effect on rat fecal microbiota fermentations and short chain fatty acids production were investigated. PHP1 was mainly composed of galactose and the main linkage types were identified as → 3)G4Sβ(1 → 3)G(1 → 6)G4Sα(1 → 4)LA(1 → 6)G4Sα(1→. The surface morphology of dried PHP1 films appears to be related to its chemical structure. PHP1 promoted the growth of both propionic acid-producing bacteria and propionic acid production, as well as influencing the composition and abundance of beneficial microbiota species in rats, which may be related to its high level of sulfation. The molecular weight of PHP1 decreased significantly after fermentation, which may result from hydrolysis of the galactan (with α- and β-linkages between galactose residues) by α- or β-galactosidase secreted by the microbiota. These results provided new insights into the structure-activity relationships between P. haitanensis polysaccharide and its regulation of microbiota in vivo.

Habitual Sleep Duration and the Colonic Mucosa-Associated Gut Microbiota in Humans-A Pilot Study

We examined the association between the colonic adherent microbiota and nocturnal sleep duration in humans. In a cross-sectional study, 63 polyp-free adults underwent a colonoscopy and donated 206 mucosal biopsies. The gut microbiota was profiled using the 16S rRNA gene sequencing targeting the V4 region. The sequence reads were processed using UPARSE and DADA2, respectively. Lifestyle factors, including sleep habits, were obtained using an interviewer-administered questionnaire. We categorized the participants into short sleepers (<6 h per night; n = 16) and normal sleepers (6–8 h per night; n = 47) based on self-reported data. Differences in bacterial biodiversity and the taxonomic relative abundance were compared between short vs. normal sleepers, followed by multivariable analysis. A false discovery rate-adjusted p value (q value) < 0.05 indicated statistical significance. The bacterial community composition differed in short and normal sleepers. The relative abundance of Sutterella was significantly lower (0.38% vs. 1.25%) and that of Pseudomonas was significantly higher (0.14% vs. 0.08%) in short sleepers than in normal sleepers (q values < 0.01). The difference was confirmed in the multivariable analysis. Nocturnal sleep duration was associated with the bacterial community composition and structure in the colonic gut microbiota in adults.

Fecal Microbiota Perspective for Evaluation of Prebiotic Potential of Bamboo Hemicellulose Hydrolysate in Mice: A Preliminary Study

Bamboo hemicellulose hydrolysate (BHH) may possess antihypercholesterolemic activity; however, this activity requires further comprehensive study to assess the prebiotic mechanisms of BHH in vivo. Here, we used high-throughput 16S rRNA gene sequencing to preliminarily investigate the correlations between BHH and the fecal microbiomes of three groups of mice fed either a normal diet, a high-fat diet, or a high-fat diet supplemented with 5% BHH for 5 weeks. Alpha diversity (within community) was nonsignificant for all groups; however, beta diversity analysis among communities showed that 5% BHH suppressed the significant changes induced by the high-fat diet. The Firmicutes/Bacteroidetes ratio, the family S24-7 within the order Bacteroidales, the family Lachnospiraceae and several cellulolytic taxa were slightly ameliorated in the BHH group. These results indicated that BHH supplementation influenced the gut bacterial community and suppressed the high-fat diet-induced alterations. Additionally, BHH significantly lowered the serum cholesterol levels and fecal pH. Improving short-chain fatty acid production for all of the bacterial communities in the mouse guts may induce this effect. Thus, the prebiotic potential of BHH should be evaluated considering the gut microbial communities and their interactions.

GABA Production by Human Intestinal Bacteroides spp.: Prevalence, Regulation, and Role in Acid Stress Tolerance

The high neuroactive potential of metabolites produced by gut microbes has gained traction over the last few years, with metagenomic-based studies suggesting an important role of microbiota-derived γ-aminobutyric acid (GABA) in modulating mental health. Emerging evidence has revealed the presence of the glutamate decarboxylase (GAD)-encoding gene, a key enzyme to produce GABA, in the prominent human intestinal genus Bacteroides. Here, we investigated GABA production by Bacteroides in culture and metabolic assays combined with comparative genomics and phylogenetics. A total of 961 Bacteroides genomes were analyzed in silico and 17 metabolically and genetically diverse human intestinal isolates representing 11 species were screened in vitro. Using the model organism Bacteroides thetaiotaomicron DSM 2079, we determined GABA production kinetics, its impact on milieu pH, and we assessed its role in mitigating acid-induced cellular damage. We showed that the GAD-system consists of at least four highly conserved genes encoding a GAD, a glutaminase, a glutamate/GABA antiporter, and a potassium channel. We demonstrated a high prevalence of the GAD-system among Bacteroides with 90% of all Bacteroides genomes (96% in human gut isolates only) harboring all genes of the GAD-system and 16 intestinal Bacteroides strains producing GABA in vitro (ranging from 0.09 to 60.84 mM). We identified glutamate and glutamine as precursors of GABA production, showed that the production is regulated by pH, and that the GAD-system acts as a protective mechanism against acid stress in Bacteroides, mitigating cell death and preserving metabolic activity. Our data also indicate that the GAD-system might represent the only amino acid-dependent acid tolerance system in Bacteroides. Altogether, our results suggest an important contribution of Bacteroides in the regulation of the GABAergic system in the human gut.

The Impact of Migration on the Gut Metagenome of South Asian Canadians

South Asian (SA) Canadian immigrants have a higher risk of developing certain immune-mediated inflammatory diseases compared to non-migrant SAs. We sought to investigate the effect of migration on the gut metagenome and to identify microbiological associations between migration and conditions that may influence the development of immune-mediated inflammatory diseases. Metagenomic analysis of 58 first-generation (GEN1) SA immigrants and 38 unrelated Canadian born children-of-immigrants (GEN2) determined that the time lived in Canada was associated with continued changes in gut microbial communities. Migration of GEN1 to Canada early in life results in a gut community with similarities to GEN2 SA Canadians and non-SA North Americans. Conversely, GEN1 immigrants who arrived recently to Canada exhibited pronounced differences from GEN2, while displaying microbial similarities to a non-migrating SA cohort. Multivariate analysis identified that community composition was primarily influenced by high abundance taxa. Prevotella copri dominated in GEN1 and non-migrant SAs. Clostridia and functionally related Bacteroidia spp. replaced P. copri dominance over generations in Canada. Mutually exclusive Dialister species occurred at differing relative abundances over time and generations in Canada. This shift in species composition is accompanied by a change in genes associated with carbohydrate utilization and short-chain fatty acid production. Total energy derived from carbohydrates compared to protein consumption was significantly higher for GEN1 recent immigrants, which may influence the functional requirements of the gut community. This study demonstrates the associations between migration and the gut microbiome, which may be further associated with the altered risk of immune-mediated inflammatory diseases observed for SA Canadians.

Microbial interaction between the succinate-utilizing bacterium Phascolarctobacterium faecium and the gut commensal Bacteroides thetaiotaomicron

A large variety of microbes are present in the human gut, some of which are considered to interact with each other. Most of these interactions involve bacterial metabolites. Phascolarctobacterium faecium hardly uses carbohydrates for growth and instead uses succinate as a substrate. This study investigated the growth behavior of the co‐culture of the succinate‐specific utilizer P. faecium and the succinogenic gut commensal Bacteroides thetaiotaomicron. Succinate production by B. thetaiotaomicron supported the growth of P. faecium and concomitant propionate production via the succinate pathway. The succinate produced was completely converted to propionate. This result was comparable with the monoculture of P. faecium in the medium supplemented with 1% (w/v) succinate. We analyzed the transcriptional response (RNA‐Seq) between the mono‐ and co‐culture of P. faecium and B. thetaiotaomicron. Comparison of the expression levels of genes of P. faecium between the mono‐ and co‐cultured conditions highlighted that the genes putatively involved in the transportation of succinate were notably expressed under the co‐cultured conditions. Differential expression analysis showed that the presence of P. faecium induced changes in the B. thetaiotaomicron transcriptional pattern, for example, expression changes in the genes for vitamin B₁₂ transporters and reduced expression of glutamate‐dependent acid resistance system‐related genes. Also, transcriptome analysis of P. faecium suggested that glutamate and succinate might be used as sources of succinyl‐CoA, an intermediate in the succinate pathway. This study revealed some survival strategies of asaccharolytic bacteria, such as Phascolarctobacterium spp., in the human gut.