Megasphaera elsdenii JCM1772T Normalizes Hyperlactate Production in the Large Intestine of Fructooligosaccharide-Fed Rats by Stimulating Butyrate Production

Unveiling the influence of a probiotic combination of Heyndrickxia coagulans and Lacticaseibacillus casei on healthy human gut microbiota using the TripleSHIME® system

Probiotics are host-friendly microorganisms that can have important health benefits in the human gut microbiota as dietary supplements. Maintaining a healthy gut microbial balance relies on the intricate interplay among the intestinal microbiota, metabolic activities, and the host's immune response. This study aims to explore if a mixture of Heyndrickxia coagulans [ATB-BCS-042] and Lacticaseibacillus casei [THT-030-401] promotes in vitro this balance in representative gut microbiota from healthy individuals using the Triple-SHIME® (Simulation of the Human Intestinal Microbial Ecosystem). Metataxonomic analysis of the intestinal microbes revealed that the probiotic mix was not causing important disruptions in the biodiversity or microbial composition of the three simulated microbiota. However, some targeted populations analyzed by qPCR were found to be disrupted at the end of the probiotic treatment or after one week of washout. Populations such as Cluster IV, Cluster XVIa, and Roseburia spp., were increased indicating a potential gut health-promoting butyrogenic effect of the probiotic supplementation. In two of the systems, bifidogenic effects were observed, while in the third, the treatment caused a decrease in bifidobacteria. For the health-detrimental biomarker Escherichia-Shigella, a mild decrease in all systems was observed in the proximal colon sections, but these genera were highly increased in the distal colon sections. By the end of the washout, Bacteroides-Prevotella was found consistently boosted, which could have inflammatory consequences in the intestinal context. Although the probiotics had minimal influence on most quantified metabolites, ammonia consistently decreased after one week of daily probiotic supplementation. In reporter gene assays, aryl hydrocarbon receptor (AhR) activation was favored by the metabolic output obtained from post-treatment periods. Exposure of a human intestinal cell model to fermentation supernatant obtained after probiotic supplementation induced a trend to decrease the mRNA expression of immunomodulatory cytokines (IL-6, IL-8). Overall, with some exceptions, a positive impact of H. coagulans and L. casei probiotic mix was observed in the three parallel experiments, despite inter-individual differences. This study might serve as an in vitro pipeline for the impact assessment of probiotic combinations on the human gut microbiota.

Structural analysis of type 3 resistant starch from Canna edulis during in vitro simulated digestion and its post-digested residue impact on human gut microbiota

Introduction

Resistant starch (RS) has garnered attention for its health benefits, including modulating the gut microbiota and promoting the production of short-chain fatty acids (SCFAs).

Methods

This study investigates structural changes of type 3 resistant starch from Canna edulis (CE) during in vitro simulated digestion and explores its health-relevant properties using healthy individuals' fecal microbiota.

Results

CE, prepared with a RS content of 59.38%, underwent a comprehensive analysis employing X-ray diffraction (XRD), fourier-transform infrared spectroscopy (FTIR), and scanning electron microscopy (SEM). During simulated digestion, XRD analysis demonstrated a significant rise in CE's relative crystallinity from 38.92 to 49.34%. SEM illustrated the transition of CE from a smooth to a rough surface, a notable morphological shift. Post-digestion, CE was introduced into microbial fermentation. Notably, propionic acid and valeric acid levels significantly increased compared to the control group. Furthere more, beneficial Bifidobacterium proliferated while pathogenic Escherichia-Shigella was suppressed. When comparing CE to the well-known functional food fructo-oligosaccharide (FOS), CE showed a specific ability to support the growth of Bifidobacterium and stimulate the production of short-chain fatty acids (SCFAs) without causing lactic acid accumulation.

Discussion

CE demonstrates potential as a functional health food, with implications for gut health enhancement and SCFAs production.

Effects on growth performance and immunity of Monopterus albus after high temperature stress

To investigate the impact of the effect of high temperature stimulation on Monopterus albus larvae after a certain period of time, five experimental groups were established at different temperatures. Then, the M. albus under high temperature stress was fed at 30°C for 70 days. After that, the growth index of the M. albus was counted and analyzed. In terms of growth index, high temperature stress had significant effects on FCR, FBW, WGR, and SGR of M. albus (p < 0.05). The SR increased after being stimulated by temperature (p < 0.1). The study revealed that liver cells of M. albus were harmed by elevated temperatures of 36°C and 38°C. In the experimental group, the activities of digestive enzymes changed in the same trend, reaching the highest point in the 32°C group and then decreasing, and the AMS activity in the 38°C group was significantly different from that in the 30°C group (p < 0.05). The activities of antioxidase in liver reached the highest at 34°C, which was significantly different from those at 30°C (p < 0.05). In addition, the expression levels of TLR1, C3, TNF-α, and other genes increased in the experimental group, reaching the highest point at 34°C, and the expression level of the IL-1β gene reached the highest point at 32°C, which was significantly different from that at 30°C (p < 0.05). However, the expression level of the IRAK3 gene decreased in the experimental group and reached its lowest point at 34°C (p < 0.05). The expression level of the HSP90α gene increased with the highest temperature stimulus and reached its highest point at 38°C (p < 0.05). In the α diversity index of intestinal microorganisms in the experimental group, the observed species, Shannon, and Chao1 indexes in the 34°C group were the highest (p < 0.05), and β diversity analysis revealed that the intestinal microbial community in the experimental group was separated after high temperature stimulation. At the phylum level, the three dominant flora are Proteus, Firmicutes, and Bacteroides. Bacteroides and Macrococcus abundance increased at the genus level, but Vibrio and Aeromonas abundance decreased. To sum up, appropriate high-temperature stress can enhance the immunity and adaptability of M. albus. These results show that the high temperature stimulation of 32°C-34°C is beneficial to the industrial culture of M. albus.

Microbial signatures and enterotype clusters in fattening pigs: implications for nitrogen utilization efficiency

As global demand for pork continues to rise, strategies to enhance nitrogen utilization efficiency (NUE) in pig farming have become vital for environmental sustainability. This study explored the relationship between the fecal microbiota, their metabolites, and NUE in crossbreed fattening pigs with a defined family structure. Pigs were kept under standardized conditions and fed in a two-phase feeding regime. In each phase, one fecal sample was collected from each pig. DNA was extracted from a total of 892 fecal samples and subjected to target amplicon sequencing. The results indicated an influence of sire, sampling period (SP), and sex on the fecal microbiota. Streptococcus emerged as a potential biomarker in comparing high and low NUE pigs in SP 1, suggesting a genetic predisposition to NUE regarding the fecal microbiota. All fecal samples were grouped into two enterotype-like clusters named cluster LACTO and cluster CSST. Pigs' affiliation with enterotype-like clusters altered over time and might be sex-dependent. The stable cluster CSST demonstrated the highest NUE despite containing pigs with lower performance characteristics such as average daily gain, dry matter intake, and daily nitrogen retention. This research contributes with valuable insights into the microbiome's role in NUE, paving the way for future strategies to enhance sustainable pig production.

Consumption of the Non-Nutritive Sweetener Stevia for 12 Weeks Does Not Alter the Composition of the Human Gut Microbiota

The use of non-nutritive sweeteners (NNSs) as an alternative to caloric sugars has increased in recent years. Stevia is an NNS that has demonstrated beneficial effects on appetite and energy intake. However, the impact on the gut microbiota is not well understood. Therefore, we investigated how regular consumption of stevia, for up to 12 weeks, impacts the human gut microbiota. Healthy subjects with a normal body mass index participated in our study; the stevia group (n = 14) was asked to consume five drops of stevia twice daily, compared to control participants (n = 13). Faecal samples collected before and after treatment were analysed by 16S rRNA gene sequencing. Stevia did not cause significant changes in the alpha or beta diversity when compared to the control groups. When the relative abundances of taxa were investigated, no clear differences were detected. Conversely, a random forest analysis correctly associated the gut microbiome with the control and stevia groups with an average of 75% accuracy, suggesting that there are intrinsic patterns that could discriminate between control and stevia use. However, large-scale changes in the gut microbiota were not apparent in this study, and, therefore, our data suggest that stevia does not significantly impact the gut microbiota.

Comparative prebiotic potential of galacto- and fructo-oligosaccharides, native inulin, and acacia gum in Kenyan infant gut microbiota during iron supplementation

Iron fortification to prevent anemia in African infants increases colonic iron levels, favoring the growth of enteropathogens. The use of prebiotics may be an effective strategy to reduce these detrimental effects. Using the African infant PolyFermS gut model, we compared the effect of the prebiotics short-chain galacto- with long-chain fructo-oligosaccharides (scGOS/lcFOS) and native inulin, and the emerging prebiotic acacia gum, a branched-polysaccharide-protein complex consisting of arabinose and galactose, during iron supplementation on four Kenyan infant gut microbiota. Iron supplementation did not alter the microbiota but promoted Clostridioides difficile in one microbiota. The prebiotic effect of scGOS/lcFOS and inulin was confirmed during iron supplementation in all investigated Kenyan infant gut microbiota, leading to higher abundance of bifidobacteria, increased production of acetate, propionate, and butyrate, and a significant shift in microbiota composition compared to non-supplemented microbiota. The abundance of the pathogens Clostridium difficile and Clostridium perfringens was also inhibited upon addition of the prebiotic fibers. Acacia gum had no effect on any of the microbiota. In conclusion, scGOS/lcFOS and inulin, but not acacia gum, showed a donor-independent strong prebiotic potential in Kenyan infant gut microbiota. This study demonstrates the relevance of comparing fibers in vitro prior to clinical studies.

Effects of Simulated In Vitro Digestion on the Structural Characteristics, Inhibitory Activity on α-Glucosidase, and Fermentation Behaviours of a Polysaccharide from Anemarrhena asphodeloides Bunge

The purpose of this study is to investigate the effects of the simulated saliva-gastrointestinal digestion of AABP-2B on its structural features, inhibitory α-glucosidase activity, and human gut microbiota. The salivary-gastrointestinal digestion results show that there is no significant change in the molecular weight of AABP-2B, and no free monosaccharides are released. This indicates that, under a simulated digestive condition, AABP-2B is not degraded and can be further utilized by gut microbiota. AABP-2B still possessed good inhibitory activity on α-glucosidase after salivary-gastrointestinal digestion, which may be attributed to the largely unchanged structural characteristics of AABP-2B after simulated digestion. Furthermore, in vitro fecal fermentation with AABP-2B after salivary-gastrointestinal digestion showed that AABP-2B modulated the gut microbiota structure and increased the relative proportions of Prevotella, Faecalibacterium, and Megasphaera. AABP-2B can also modify the intestinal flora composition by inhibiting pathogen growth. Moreover, the AABP-2B group resulted in a significant increase in short-chain fatty acid (SCFAs) content during fermentation. These findings demonstrate that AABP-2B can be used as a prebiotic or functional food to promote gut health.

Fermented Vegetables as a Potential Treatment for Irritable Bowel Syndrome

Foods and supplements containing microorganisms with expected beneficial effects are increasingly investigated and utilized in the treatment of human illness, including irritable bowel syndrome (IBS). Research points to a prominent role of gut dysbiosis in the multiple aberrations in gastrointestinal function, immune balance, and mental health seen in IBS. The proposition of the current Perspective is that fermented vegetable foods, in combination with a healthy and stable diet, may be particularly useful for addressing these disturbances. This is based on the recognition that plants and their associated microorganisms have contributed to shaping human microbiota and adaptation over evolutionary time. In particular, lactic acid bacteria with immunomodulatory, antipathogenic, and digestive properties are prevalent in products such as sauerkraut and kimchi. Additionally, by adjusting the salt content and fermentation time, products with a microbial and therapeutic potential beyond that of regular ferments could potentially be produced. Although more clinical data are required to make firm assertions, the low-risk profile, combined with biological considerations and reasoning and considerable circumstantial and anecdotal evidence, indicate that fermented vegetables are worthy of consideration by health professionals and patients dealing with IBS-related issues. To maximize microbial diversity and limit the risk of adverse effects, small doses of multiple products, containing different combinations of traditionally fermented vegetables and/or fruits, is suggested for experimental research and care.

Effects of in vitro digestion and fecal fermentation on physico-chemical properties and metabolic behavior of polysaccharides from Clitocybe squamulosa

The aim of this study was to establish a human digestion model in vitro to explore the degradation characteristics of a novel high-purity polysaccharide from Clitocybe squamulosa (CSFP2). The results showed that the content of reducing sugars (C_R ) of CSFP2 increased from 0.13 to 0.23 mg/mL, the molecular weight (Mw) of CSFP2 decreased significantly during the saliva-gastrointestinal digestion. The constituent monosaccharides of CSFP2, including galactose, glucose, and mannose, were stable during in vitro digestion, but their molar ratios were changed from 0.023: 0.737: 0.234 to 0.496: 0.478: 0.027. The surface of CSFP2 changes from a rough flaky structure to a scattered flocculent or rod-shaped structure after the gastrointestinal digestion. However, the apparent viscosity of CSFP2 was overall stable during in vitro digestion. Moreover, CSFP2 still maintains its strong antioxidant capacity after saliva-gastrointestinal digestion. The results showed that CSFP2 can be partially decomposed during digestion. Meanwhile, some physico-chemical properties of the fermentation broth containing CSFP2 changed significantly after gut microbiota fermentation. For example, the pH value (from 8.46 to 4.72) decreased significantly (p < 0.05) after 48 h of fermentation. the OD ₆₀₀ value increased first and then decreased (from 2.00 to 2.68 to 1.32) during 48-h fermentation. In addition, CSFP2 could also increase the amounts of short-chain fatty acids (SCFAs) (from 5.5 to 37.15 mmol/L) during fermentation (in particular, acetic acid, propionic acid, and butyric acid). Furthermore, the relative abundances of Bacteriodes, Bifidobacterium, Catenibacterium, Lachnospiraceae_NK4A136_group, Megasphaera, Prevotella, Megamonas, and Lactobacillus at genus level were markedly increased with the intervention of CSFP2. These results provided a theoretical basis for the further development of functional foods related to CSFP2.

Can dietary magnesium sources and buffer change the ruminal microbiota composition and fermentation of lactating dairy cows?

Magnesium oxide (MgO) is one of the most used Mg supplements in livestock. However, to avoid relying upon only one Mg source, it is important to have alternative Mg sources. Therefore, the objective of this study was to evaluate the effects of the interaction of two Mg sources with buffer use on the ruminal microbiota composition, ruminal fermentation, and nutrient digestibility in lactating dairy cows. Twenty lactating Holstein cows were blocked by parity and days in milk into five blocks with four cows each, in a 2 × 2 factorial design. Within blocks, cows were assigned to one of four treatments: 1) MgO; 2) MgO + Na sesquicarbonate (MgO+); 3) calcium-magnesium hydroxide (CaMgOH); 4) CaMgOH + Na sesquicarbonate (CaMgOH+). For 60 d, cows were individually fed a corn silage-based diet, and treatments were top-dressed. Ruminal fluid was collected via an orogastric tube, for analyses of the microbiota composition, volatile fatty acids (VFA), lactate, and ammonia nitrogen (NH3-N). The microbiota composition was analyzed using V4/16S rRNA gene sequencing, and taxonomy was assigned using the Silva database. Statistical analysis was carried out following the procedures of block design analysis, where block and cow were considered random variables. Effects of Mg source, buffer, and the interaction between Mg Source × Buffer were analyzed through orthogonal contrasts. There was no interaction effect of the two factors evaluated. There was a greater concentration of NH3-N, lactate, and butyrate in the ruminal fluid of cows fed with CaMg(OH)2, regardless of the buffer use. The increase in these fermentation intermediates/ end-products can be explained by an increase in abundance of micro-organisms of the genus Prevotella, Lactobacillus, and Butyrivibrio, which are micro-organisms mainly responsible for proteolysis, lactate-production, and butyrate-production in the rumen, respectively. Also, dietary buffer use did not affect the ruminal fermentation metabolites and pH; however, an improvement of the apparent total tract digestibility of dry matter (DM), organic matter (OM), neutral fiber detergent (NDF), and acid fiber detergent (ADF) were found for animals fed with dietary buffer. In summary, there was no interaction effect of buffer use and Mg source, whereas buffer improved total tract apparent digestibility of DM and OM through an increase in NDF and ADF digestibility and CaMg(OH)2 increased ruminal concentration of butyrate and abundance of butyrate-producing bacteria.

Effect of dietary calcium concentration and exogenous phytase on inositol phosphate degradation, mineral digestibility, and gut microbiota in growing pigs

Variations in the dietary Ca concentration may affect inositol phosphate (InsP) degradation, and thereby, P digestibility in pigs. This study assessed the effects of dietary Ca concentration and exogenous phytase on InsP degradation, nutrient digestion and retention, blood metabolites, and microbiota composition in growing pigs with ileal cannulation. In a completely randomized row-column design with four periods, eight ileal-cannulated barrows (initial body weight 27 kg) were fed four corn-soybean- and rapeseed meal-based diets containing 5.5 or 8.5 g Ca/kg dry matter (DM), with or without 1,500 FTU of an exogenous hybrid-6-phytase/kg diet. No mineral P was added and the P concentration in the feed was 4.8 g P/kg DM. Prececal InsP6 disappearance in pigs fed diets containing exogenous phytase was lower (P = 0.022) with additional Ca than without. Concentrations of InsP2-4 isomers and myo-inositol in the distal ileal digesta and prececal P digestibility were greater (P < 0.001) with exogenous phytase than without exogenous phytase. In feces, InsP6 disappearance was lower (P < 0.002) and concentration of InsP5 and InsP4 isomers was higher (P ≤ 0.031) with additional Ca compared to without additional Ca. The prececal amino acid digestibility, energy digestibility, and hindgut disappearance of energy did not differ. The Shannon diversity index of the microbiota in the distal ileal digesta and feces was similar among the diets but was lower in the distal ileal digesta than in the feces (P < 0.001). Permutation analysis of variance revealed no dietary differences between the bacterial groups within the ileal digesta and fecal samples (P > 0.05). In conclusion, additional Ca reduced the effect of exogenous phytase on prececal InsP6 degradation. Endogenous InsP degradation was impaired by additional Ca only in the hindgut but the abundance of bacterial genera in feces was not affected.

[Diversity and functional prediction of gut microbiota in children with autism spectrum disorder]

OBJECTIVES

To study the structure and diversity of gut microbiota in children with autism spectrum disorder (ASD), and to predict the metabolic function of gut microbiota.

METHODS

Fecal samples were collected from 30 ASD children (ASD group) and 20 typically developing (TD) children (TD group). Genomic DNA was extracted, the 16S rDNA V4 region was amplified by PCR, and Illumina NovaSeq6000 platform was used for high-throughput sequencing. The composition and distribution characteristics of gut microbiota were analyzed for the two groups, and the metabolic function of gut microbiota was predicted.

RESULTS

There were no significant differences in alpha diversity indices (Chao1, Shannon, and Simpson) of gut microbiota between the ASD and TD groups (P>0.05). At the phylum and class levels, there was no significant difference in the structure of gut microbiota between the two groups (P>0.05). Compared with the TD group, the ASD group had significantly higher abundance of Megamonas, Barnesiella, Dialister, Megasphaera, Ruminococcus_torques_group, and Fusobacterium at the genus level (P<0.05). Functional prediction analysis showed that compared with the TD group, the ASD group had a significantly lower abundance of the gut microbiota with the metabolic functions such as tryptophan degradation, glutamate degradation, and butyrate production (P<0.05) and a significantly higher abundance of the gut microbiota with the metabolic function of GABA degradation (P<0.05).

CONCLUSIONS

There is no significant difference in the alpha diversity of gut microbiota between ASD children and TD children, while there are differences in the composition of species at the genus level and the metabolic functions of gut microbiota.

In Vitro Digestion and Fecal Fermentation of Peach Gum Polysaccharides with Different Molecular Weights and Their Impacts on Gut Microbiota

In the present study, we investigated the in vitro digestion and fermentation characteristics of three peach gum polysaccharides (PGPs) of different molecular weights; i.e., AEPG2 (1.64 × 107 g/mol), DPG2 (5.21 × 105 g/mol), and LP100R (8.50 × 104 g/mol). We observed that PGPs were indigestible during the oral, gastrointestinal, and intestinal stages. However, they were utilized by the gut microbiota with utilization rates in the order of DPG2 > AEPG2 > LP100R. Furthermore, arabinose in PGPs was preferentially utilized by the gut microbiota followed by galactose and xylose. Fermentation of peach gum polysaccharides could significantly increase the production of short-chain fatty acids (SCFAs), especially n-butyric acid. In addition, PGPs with different molecular weights values were predominantly fermented by different bacterial species. AEPG2 and DPG2 were fermented by the Bacteroidetes bacteria Bacteroides, while the dominant n-butyrate-producing bacteria was Faecalibacterium. While the LP100R was fermented by Bacteroides, Parabacteroides, Phascolarctobacterium, Dialister, Lachnospiraceae, and Blautia, the dominant n-butyrate-producing bacteria was Megamonas. These results indicated that PGPs are potential prebiotics for the food industry.

Association of key species of vaginal bacteria of recurrent bacterial vaginosis patients before and after oral metronidazole therapy with short- and long-term clinical outcomes

Bacterial vaginosis (BV) is associated with a state of vaginal dysbiosis typically involving depletion of otherwise dominant populations of Lactobacillus. The causes of this microbial succession are not known; there may be multiple causes. Standard treatment includes oral metronidazole, which typically restores Lactobacillus species to dominance. However, recurrence rates are high; recurrent BV patients recur 3–4 times annually and are often refractory to treatment. Our previous qPCR-based study of recurrent BV patients pointed to putatively more virulent species of Gardnerella that were associated with refractory responses to oral metronidazole, and less robust recovery of Lactobacillus species associated with recurrence after an initial period of remission. However, these associations did not account for outcomes in all patients, suggesting that other bacterial species were involved. In this follow-up study, we sequenced the V4 domain of 16S rRNA sequences of 41of these same patients pre- and posttreatment. Overall compositions among pretreatment clinical outcome groups were not different, although alpha diversity significantly decreased: refractory > recurrent > remission. Combinations of key species were associated with and prognostic for outcome. Higher pretreatment abundance of Megasphaera lornae together with lower abundance of Gardnerella Gsp07 and Finegoldia magna predicted long term remission after oral metronidazole. Furthermore, a subset of refractory patients that did not have high levels of Gardnerella Gsp07, instead had elevated levels of alternative species including Atopobium vaginae, Mageeibacillus indolicus (BVAB3), and Prevotella timonensis. Patients who recurred after transient remission had elevated abundance of species including Atopobium vaginae, Gardnerella, and Aerococcus christensenii, compared to long-term remission patients. Core bacterial species among refractory patients did not change in abundance after metronidazole, suggesting resistance or tolerance, in contrast to the loss in abundance of the same species among recurrent or remission patients. These findings have potential prognostic and therapeutic implications.

The Distinguishing Bacterial Features From Active and Remission Stages of Ulcerative Colitis Revealed by Paired Fecal Metagenomes

Ulcerative colitis (UC) is a serious chronic intestinal inflammatory disease, with an increased incidence in recent years. The intestinal microbiota plays a key role in the pathogenesis of UC. However, there is no unified conclusion on how the intestinal microbiota changes. Most studies focus on the change between UC patients and healthy individuals, rather than the active and remission stage of the same patient. To minimize the influences of genetic differences, environmental and dietary factors, we studied the intestinal microbiota of paired fecal samples from 42 UC patients at the active and remission stages. We identified 175 species of microbes from 11 phyla and found no difference of the alpha and beta diversities between the active and remission stages. Paired t-test analysis revealed differential microbiota at levels of the phyla, class, order, family, genus, and species, including 13 species with differential abundance. For example, CAG-269 sp001916005, Eubacterium F sp003491505, Lachnospira sp000436475, et al. were downregulated in the remission, while the species of Parabacteroides distasonis, Prevotellamassilia sp900540885, CAG-495 sp001917125, et al. were upregulated in the remission. The 13 species can effectively distinguish the active and remission stages. Functional analysis showed that the sporulation and biosynthesis were downregulated, and the hydrogen peroxide catabolic process was upregulated in remission of UC. Our study suggests that the 13 species together may serve as a biomarker panel contributing to identify the active and remission stages of UC, which provides a valuable reference for the treatment of UC patients by FMT or other therapeutic methods.

Characteristics of the gut microbiota in women with premenstrual symptoms: A cross-sectional study

Purpose

Premenstrual symptoms can negatively impact the quality of life of women through a range of mood, behavioral, and physical symptoms. The association between the microbiota and brain function has been extensively studied. Here, we examined the characteristics of the microbiota in women with premenstrual disorders (PMDs) and the association between premenstrual symptoms and the microbiota.

Materials and methods

In this single center cross-sectional pilot study, we recruited 27 women reporting premenstrual symptoms and 29 women with no serious premenstrual symptoms. Among them, we further selected 21 women experiencing premenstrual symptoms resulting in interference to their social life (PMDs group) and 22 women with no serious premenstrual symptoms and thereby no interference to their social life (control group). The severity of symptoms was evaluated by a premenstrual symptoms questionnaire (PSQ). Inflammatory markers were analyzed in blood samples, including C reactive protein, soluble CD14, and lipopolysaccharide binding protein. Sequencing of 16S ribosomal ribonucleic acid genes was performed on stool samples.

Results

Inflammatory markers in blood samples did not differ significantly between the PMDs and control groups. A difference in beta, but not alpha diversity, was detected for the gut microbiotas of the PMDs and control groups. The relative abundance of the Bacteroidetes phylum was lower in the PMDs group. At the genus level, the prevalence was decreased for Butyricicoccus, Extibacter, Megasphaera, and Parabacteroides and increased for Anaerotaenia in the PMDs group, but after false discovery rate correction, these differences were no longer significant. Linear discriminant effect size analysis revealed a decrease in Extibacter, Butyricicoccus, Megasphaera, and Parabacteroides and an increase in Anaerotaenia in the PMDs group. The PSQ total score correlated with Anaerotaenia, Extibacter, and Parabacteroides. Multiple regression analysis showed that Parabacteroides and Megasphaera negatively predicted the PSQ total score.

Conclusion

The properties of the gut microbiota are associated with premenstrual symptoms.

Chlorella pyrenoidosa Polysaccharides as a Prebiotic to Modulate Gut Microbiota: Physicochemical Properties and Fermentation Characteristics In Vitro

This study was conducted to investigate the prebiotic potential of Chlorella pyrenoidosa polysaccharides to provide useful information for developing C. pyrenoidosa as a green healthy food. C. pyrenoidosa polysaccharides were prepared and their physicochemical characteristics were determined. The digestibility and fermentation characteristics of C. pyrenoidosa polysaccharides were evaluated using in vitro models. The results revealed that C. pyrenoidosa polysaccharides were composed of five non-starch polysaccharide fractions with monosaccharide compositions of Man, Rib, Rha, GlcA, Glc, Gal, Xyl and Ara. C. pyrenoidosa polysaccharides could not be degraded under saliva and the gastrointestinal conditions. However, the molecular weight and contents of residual carbohydrates and reducing sugars of C. pyrenoidosa polysaccharides were significantly reduced after fecal fermentation at a moderate speed. Notably, C. pyrenoidosa polysaccharides could remarkably modulate gut microbiota, including the promotion of beneficial bacteria, inhibition of growth of harmful bacteria, and reduction of the ratio of Firmicutes to Bacteroidetes. Intriguingly, C. pyrenoidosa polysaccharides can promote growth of Parabacteroides distasonis and increase short-chain fatty acid contents, thereby probably contributing to the promotion of intestinal health and prevention of diseases. Thus, these results suggested that C. pyrenoidosa polysaccharides had prebiotic functions with different fermentation characteristics compared with conventional prebiotics such as fructooligosaccharide, and they may be a new prebiotic for improving human health.

Microorganisms in Whole Botanical Fermented Foods Survive Processing and Simulated Digestion to Affect Gut Microbiota Composition

Botanical fermented foods have been shown to improve human health, based on the activity of potentially beneficial lactic acid bacteria (LAB) and yeasts and their metabolic outputs. However, few studies have explored the effects of prolonged storage and functional spices on microbial viability of whole fermented foods from fermentation to digestion. Even fewer have assessed their impact on the gut microbiota. Our study investigated the effects of production processes on LAB and yeast microbial viability and gut microbiota composition. We achieved this by using physicochemical assessments and an in vitro gastrointestinal and a porcine gut microbiota model. In low-salt sauerkraut, we assessed the effects of salt concentration, starter cultures, and prolonged storage, and in tibicos, prolonged storage and the addition of spices cayenne, ginger, and turmeric. In both food matrices, LAB counts significantly increased (p<0.05), reaching a peak of 7–8 log cfu/g, declining to 6–6.5 log cfu/g by day 96. Yeast viability remained at 5–6 log cfu/g in tibicos. Ginger tibicos had significantly increased LAB and yeast viability during fermentation and storage (p<0.05). For maximum microbial consumption, tibicos should be consumed within 28days, and sauerkraut, 7weeks. Simulated upper GI digestion of both products resulted in high microbial survival rates of 70–80%. The 82% microbial survival rate of cayenne tibicos was significantly higher than other treatments (p<0.05). 16S rRNA sequencing of simulated porcine colonic microbiota showed that both spontaneously fermented sauerkraut and tibicos increase the relative abundance of Megasphaera 85-fold. These findings will inform researchers, producers, and consumers about the factors that affect the microbial content of fermented foods, and their potential effects on the gut.

Biohydrogen production by mixed culture of Megasphaera elsdenii with lactic acid bacteria as Lactate-driven dark fermentation

Numerous attempts have been made to upscale biohydrogen production via dark fermentation (DF); however, the Achilles' heel of DF, i.e., lactic acid bacteria (LAB) contamination and overgrowth, hinders such upscaling. Key microbes are needed to develop a lactate-driven DF system that can serve as a lactate fermentation platform. In this study, the utility of Megasphaera elsdenii and LAB co-culturing in lactate-driven DF was evaluated. When inoculated simultaneously with LAB or after LAB culture, M. elsdenii achieved a stable hydrogen yield of 0.95-1.49 H₂-mol/mol-glucose, approximately half that obtained in pure M. elsdenii cultures. Hydrogen production was maintained even at an initial M. elsdenii-to-LAB cell ratio of one-millionth or less. Moreover, M. elsdenii produced hydrogen via lactate-driven DF from unusable sugars such as xylose or cellobiose. Thus, M. elsdenii could be a Game changer instrumental in unlocking the full potential of DF.

Dynamics of dark fermentation microbial communities in the light of lactate and butyrate production

BACKGROUND

This study focuses on the processes occurring during the acidogenic step of anaerobic digestion, especially resulting from nutritional interactions between dark fermentation (DF) bacteria and lactic acid bacteria (LAB). Previously, we have confirmed that DF microbial communities (MCs) that fed on molasses are able to convert lactate and acetate to butyrate. The aims of the study were to recognize the biodiversity of DF-MCs able and unable to convert lactate and acetate to butyrate and to define the conditions for the transformation.

RESULTS

MCs sampled from a DF bioreactor were grown anaerobically in mesophilic conditions on different media containing molasses or sucrose and/or lactate and acetate in five independent static batch experiments. The taxonomic composition (based on 16S_rRNA profiling) of each experimental MC was analysed in reference to its metabolites and pH of the digestive liquids. In the samples where the fermented media contained carbohydrates, the two main tendencies were observed: (i) a low pH (pH ≤ 4), lactate and ethanol as the main fermentation products, MCs dominated with Lactobacillus, Bifidobacterium, Leuconostoc and Fructobacillus was characterized by low biodiversity; (ii) pH in the range 5.0-6.0, butyrate dominated among the fermentation products, the MCs composed mainly of Clostridium (especially Clostridium_sensu_stricto_12), Lactobacillus, Bifidobacterium and Prevotella. The biodiversity increased with the ability to convert acetate and lactate to butyrate. The MC processing exclusively lactate and acetate showed the highest biodiversity and was dominated by Clostridium (especially Clostridium_sensu_stricto_12). LAB were reduced; other genera such as Terrisporobacter, Lachnoclostridium, Paraclostridium or Sutterella were found. Butyrate was the main metabolite and pH was 7. Shotgun metagenomic analysis of the selected butyrate-producing MCs independently on the substrate revealed C.tyrobutyricum as the dominant Clostridium species. Functional analysis confirmed the presence of genes encoding key enzymes of the fermentation routes.

CONCLUSIONS

Batch tests revealed the dynamics of metabolic activity and composition of DF-MCs dependent on fermentation conditions. The balance between LAB and the butyrate producers and the pH values were shown to be the most relevant for the process of lactate and acetate conversion to butyrate. To close the knowledge gaps is to find signalling factors responsible for the metabolic shift of the DF-MCs towards lactate fermentation. Video Abstract.

Effects of Clostridium butyricum on growth performance, metabonomics and intestinal microbial differences of weaned piglets

Background

Weaning stress of piglets causes a huge economic loss to the pig industry. Balance and stability of the intestinal microenvironment is an effective way to reduce the occurance of stress during the weaning process. Clostridium butyricum, as a new microecological preparation, is resistant to high temperature, acid, bile salts and some antibiotics. The aim of present study is to investigate the effects of C. butyricum on the intestinal microbiota and their metabolites in weaned piglets.

Results

There was no statistical significance in the growth performance and the incidence of diarrhoea among the weaned piglets treated with C. butyricum during 0–21 days experimental period. Analysis of 16S rRNA gene sequencing results showed that the operational taxonomic units (OTUs), abundance-based coverage estimator (ACE) and Chao index of the CB group were found to be significantly increased compared with the NC group (P < 0.05). Bacteroidetes, Firmicutes and Tenericutes were the predominant bacterial phyla in the weaned piglets. A marked increase in the relative abundance of Megasphaera, Ruminococcaceae_NK4A214_group and Prevotellaceae_UCG-003, along with a decreased relative abundance of Ruminococcaceae_UCG-005 was observed in the CB group, when compared with the NC group (P < 0.05). With the addition of C. butyricum, a total of twenty-two significantly altered metabolites were obtained in the feces of piglets. The integrated pathway analysis by MetaboAnalyst indicated that arginine and proline metabolism; valine, leucine and isoleucine biosynthesis; and phenylalanine metabolism were the main three altered pathways, based on the topology. Furthermore, Spearman’s analysis revealed some altered gut microbiota genus such as Oscillospira, Ruminococcaceae_NK4A214_group, Megasphaera, Ruminococcaceae_UCG-005, Prevotella_2, Ruminococcaceae_UCG-002, Rikenellaceae_RC9_gut_group and Prevotellaceae_UCG-003 were associated with the alterations in the fecal metabolites (P < 0.05), indicating that C. butyricum presented a potential protective impact through gut microbiota. The intestinal metabolites changed by C. butyricum mainly involved the variation of citrulline, dicarboxylic acids, branched-chain amino acid and tryptophan metabolic pathways.

Conclusions

Overall, this study strengthens the idea that the dietary C. butyricum treatment can significantly alter the intestinal microbiota and metabolite profiles of the weaned piglets, and C. butyricum can offer potential benefits for the gut health.

Impact of the factors shaping gut microbiota on obesity

Obesity is considered as a risk factor for chronic health diseases such as heart diseases, cancer and diabetes 2. Reduced physical activities, lifestyle, poor nutritional diet and genetics are among the risk factors associated with the development of obesity. In recent years, several studies have explored the link between the gut microbiome and the progression of diseases including obesity, with the shift in microbiome abundance and composition being the main focus. The alteration of gut microbiome composition affects both nutrients metabolism and specific gene expressions, thereby disturbing body physiology. Specifically, the abundance of fibre-metabolizing microbes is associated with weight loss and that of protein and fat-metabolizing bacteria with weight gain. Various internal and external factors such as genetics, maternal obesity, mode of delivery, breastfeeding, nutrition, antibiotic use and the chemical compounds present in the environment are known to interfere with the richness of the gut microbiota (GM), thus influencing weight gain/loss and ultimately the development of obesity. However, the effectiveness of each factor in potentiating the shift in microbes' abundance to result in significant changes that can lead to obesity is not yet clear. In this review, we will highlight the factors involved in shaping GM, their influence on obesity and possible interventions. Understanding the influence of these factors on the diversity of the GM and how to improve their effectiveness on disease conditions could be keys in the treatment of metabolic diseases.

Diet Rich in Simple Sugars Promotes Pro-Inflammatory Response via Gut Microbiota Alteration and TLR4 Signaling

Diet is a strong modifier of microbiome and mucosal microenvironment in the gut. Recently, components of western-type diets have been associated with metabolic and immune diseases. Here, we studied how high-sugar diet (HSD) consumption influences gut mucosal barrier and immune response under steady state conditions and in a mouse model of acute colitis. We found that HSD significantly increased gut permeability, spleen weight, and neutrophil levels in spleens of healthy mice. Subsequent dextran sodium sulfate administration led to severe colitis. In colon, HSD significantly promoted neutrophil infiltration and increased the levels of IL-6, IL-1β, and TNF-α. Moreover, HSD-fed mice had significantly higher abundance of pathobionts, such as Escherichia coli and Candida, in fecal samples. Although germ-free mice colonized with microbiota of conventionally reared mice that consumed different diets had equally severe colitis, mice colonized with HSD microbiota showed markedly increased infiltration of neutrophils to the gut. The induction of colitis in Toll-like receptor 4 (TLR4)-deficient HSD-fed mice led to significantly milder colitis than in wild-type mice. In conclusion, our results suggested a significant role of HSD in disruption of barrier integrity and balanced mucosal and systemic immune response. In addition, these processes seemed to be highly influenced by resident potentially pathogenic microbiota or metabolites via the TLR4 signaling pathway.

Fermentation Ability of Gut Microbiota of Wild Japanese Macaques in the Highland and Lowland Yakushima: In Vitro Fermentation Assay and Genetic Analyses

Wild Japanese macaques (Macaca fuscata Blyth) living in the highland and lowland areas of Yakushima are known to have different diets, with highland individuals consuming more leaves. We aim to clarify whether and how these differences in diet are also reflected by gut microbial composition and fermentation ability. Therefore, we conduct an in vitro fermentation assay using fresh feces from macaques as inoculum and dry leaf powder of Eurya japonica Thunb. as a substrate. Fermentation activity was higher for feces collected in the highland, as evidenced by higher gas and butyric acid production and lower pH. Genetic analysis indicated separation of highland and lowland in terms of both community structure and function of the gut microbiota. Comparison of feces and suspension after fermentation indicated that the community structure changed during fermentation, and the change was larger for lowland samples. Analysis of the 16S rRNA V3-V4 barcoding region of the gut microbiota showed that community structure was clearly clustered between the two areas. Furthermore, metagenomic analysis indicated separation by gene and pathway abundance patterns. Two pathways (glycogen biosynthesis I and D-galacturonate degradation I) were enriched in lowland samples, possibly related to the fruit-eating lifestyle in the lowland. Overall, we demonstrated that the more leaf-eating highland Japanese macaques harbor gut microbiota with higher leaf fermentation ability compared with the more fruit-eating lowland ones. Broad, non-specific taxonomic and functional gut microbiome differences suggest that this pattern may be driven by a complex interplay between many taxa and pathways rather than single functional traits.

Metabolomic LC-MS/MS analyses and meta 16S rRNA gene analyses on cecal feces of Japanese rock ptarmigans reveal fundamental differences between semi-wild and captive raised individuals

Ex situ conservation of Japanese rock ptarmigans began in 2015 with the aim of reintroducing artificially raised birds into their original habitat. However, the current raising method in captivity seems insufficient in terms of the survivability of artificially raised birds in natural conditions. Feeding management is one potential reason for such insufficiency. In this study, we performed a comprehensive analysis of the hydrophilic metabolites by LC-MS/MS for the cecal feces of Japanese rock ptarmigans under in situ and ex situ conservation to reveal their gut chemical environment. We also analyzed the developmental processes of cecal microbiomes both in situ semi-wild and ex situ captive individuals. Metabolites of nucleic acid were rich in the in situ individuals, and free amino acids were rich in the ex situ individuals. The differences in the microbiome composition between in situ and ex situ individuals were also pronounced; major genera of in situ individuals were not detected or few in ex situ individuals. The alpha diversity of the cecal microbiome of semi-wild chicks at 1 week of age was almost the same as that of their hens, while it was very low in captive individuals. Sub-therapeutic use of oxytetracycline, a diet rich in protein and energy, and isolation from adult birds are considered to be causes for these great differences in gut chemical and microbiological environment between in situ and ex situ individuals.

Activation of butyrate-producing bacteria as well as bifidobacteria in the cat intestinal microbiota by the administration of 1-kestose, the smallest component of fructo-oligosaccharide

1-kestose is a structural component of fructo-oligosaccharides and is composed of 2 fructose residues bound to sucrose through β2-1 bonds. In the present study, the influence of the ingestion of 1-kestose on the intestinal microbiota was investigated in cats. Six healthy cats were administered 1 g/day of 1-kestose for 8 weeks followed by a 2-week wash-out period. Fecal samples were collected from cats after 0, 4, 8, and 10 weeks. The intestinal microbiota was examined by a 16S rRNA gene metagenomic analysis and real-time PCR. Short-chain fatty acids were measured by GC/MS. The results suggested that the intestinal bacterial community structure in feline assigned to this study was divided into 2 types: one group mainly composed of the genus Lactobacillus (GA) and the other mainly composed of the genus Blautia with very few bacteria of Lactobacillus (GB). Furthermore, the number of Bifidobacterium slightly increased after the administration of 1-kestose (at 4 and 8 weeks) (P<0.1). The administration of 1-kestose also increased the abundance of Megasphaera, the butyric acid-producing bacteria, at 4 and 8 weeks (P<0.1). Furthermore, an increase in butyric acid levels was observed after the administration of 1-kestose for 4 weeks (P<0.1). These results suggest that 1-kestose activated butyrate-producing bacteria as well as bifidobacteria and propose its potential as a new generation prebiotic.

Co-occurrence of Campylobacter Species in Children From Eastern Ethiopia, and Their Association With Environmental Enteric Dysfunction, Diarrhea, and Host Microbiome

High Campylobacter prevalence during early childhood has been associated with stunting and environmental enteric dysfunction (EED), especially in low resource settings. This study assessed the prevalence, diversity, abundance, and co-occurrence of Campylobacter spp. in stools from children in a rural area of eastern Ethiopia and their association with microbiome, diarrhea, and EED in children. Stool samples (n = 100) were collected from randomly selected children (age range: 360-498 days) in five kebeles in Haramaya District, Ethiopia. Diarrhea, compromised gut permeability, and gut inflammation were observed in 48, 45, and 57% of children, respectively. Campylobacter prevalence and species diversity were assessed using PCR and meta-total RNA sequencing (MeTRS). The prevalence of Campylobacter spp. in the children's stools was 50% (41-60%) by PCR and 88% (80-93.6%) by MeTRS (P < 0.01). Further, seven Campylobacter species (Campylobacter jejuni, Campylobacter upsaliensis, Campylobacter hyointestinalis, Campylobacter coli, Campylobacter sp. RM6137, uncultured Campylobacter sp., and Campylobacter sp. RM12175) were detected by MeTRS in at least 40% of children stools in high abundance (>1.76-log read per million per positive stool sample). Four clusters of Campylobacter species (5-12 species per cluster) co-occurred in the stool samples, suggesting that Campylobacter colonization of children may have occurred through multiple reservoirs or from a reservoir in which several Campylobacter species may co-inhabit. No associations between Campylobacter spp., EED, and diarrhea were detected in this cross-sectional study; however, characteristic microbiome profiles were identified based on the prevalence of Campylobacter spp., EED severity, and diarrhea. Forty-seven bacterial species were correlated with Campylobacter, and 13 of them also correlated with gut permeability, gut inflammation and/or EED severity. Forty-nine species not correlated with Campylobacter were correlated with gut permeability, gut inflammation, EED severity and/or diarrhea. This study demonstrated that (1) in addition to C. jejuni and C. coli, multiple non-thermophilic Campylobacter spp. (i.e., Campylobacter hyointestinalis, Campylobacter fetus, and Campylobacter concisus) were frequently detected in the children's stools and (2) the Campylobacter, gut permeability, gut inflammation, EED severity, and diarrhea were associated with characteristic microbiome composition. Additional spatial and longitudinal studies are needed to identify environmental reservoirs and sources of infection of children with disparate Campylobacter species and to better define their associations with EED in low-income countries.

ZnO Modulates Swine Gut Microbiota and Improves Growth Performance of Nursery Pigs When Combined with Peptide Cocktail

Zinc has been very efficacious in reducing post-weaning diarrhea, whereas animal-derived peptides are suggested to improve the growth performance of weaned piglets. However, the combined effect of zinc and peptides on swine production and swine gut microbiota is still largely unknown. In this study, we followed 288 nursery pigs from the age of d30 to d60 to evaluate the growth performance and gut microbiota of weanling pigs subjected to different levels of a fish-porcine-microbial peptide cocktail (0.05%, 0.25%, and 0.5%) with or without the pharmaceutical level of zinc oxide (ZnO) (2500 ppm) supplementation in a nutrient-deficient diet. Rectal swab samples were collected from pigs with body weight (BW) approach average at each pen on d30, d42, and d60 to determine gut microbiota. Average daily gain (ADG) and BW in piglets fed high zinc (HZ) increased with increasing levels of peptide. The microbiota of the HZ group also diverged from those of the standard zinc (SZ) group from d30 to d60. Adding peptide did not alter community structure regardless of zinc supplementation. Collectively, these findings demonstrated that the pharmaceutical level of zinc as ZnO conditioned the gut community to the point where peptide could effectively restore growth performance in nursery pigs fed nutrient-deficient diets.

Role of coprophagy in the cecal microbiome development of an herbivorous bird Japanese rock ptarmigan

The transgenerational maintenance of symbiotic microbes that benefit host nutrition and health is evolutionarily advantageous. In some vertebrate lineages, coprophagy is used as a strategy for effectively transmitting microbes across generations. However, this strategy has still not been studied in birds. Accordingly, the aim of the present study was to evaluate the role of maternal cecal feces consumption by Japanese rock ptarmigan (Lagopus muta japonica) chicks as a strategy for acquiring essential gut microbes. Both the duration of coprophagy behavior by the chicks and the development process of the chick cecal microbiome (n=20 one- to three-week-old chicks, from three broods) were investigated. In all three broods, coprophagy behavior was only observed from 3 to 18 days of age. Furthermore, there was no significant difference in the number of bacterial operational taxonomic units (OTUs) in 1-week-old chicks (n=651) and adults (n=609), and most of the main OTUs observed in the adults were already present in the 1-week-old chicks. These results indicate that, in this precocial bird species, coprophagy may contribute to the early establishment of cecal bacteria that are essential for food digestion and, thus, chick survival. In fact, Japanese rock ptarmigan chicks consume the same food as their hens from the time of hatching. This behavior may have applications to ex-situ conservation.

In vitro fermentation of copra meal hydrolysate by human fecal microbiota

Copra meal hydrolysate (CMH) is obtained by hydrolyzing defatted copra meal with β-mannanase from Bacillus circulans NT 6.7. In this study, we investigated the resistance of CMH to upper gastrointestinal tract digestion and the fecal fermentation profiles of CMH. Fecal slurries from four healthy human donors were used as inocula, and fructooligosaccharides (FOS) were used as a positive prebiotic control. Fecal batch cultures were performed at 37 °C under anaerobic conditions. Samples were collected at 0, 10, 24 and 34 h for bacterial enumeration via fluorescent in situ hybridization and organic acid (OA) analysis. In vitro gastric stomach and human pancreatic α-amylase simulations demonstrated that CMH was highly resistant to hydrolysis. Acetate was the main fermentation product of all the substrates. The proportions of acetate production of the total OAs from FOS, CMH and yeast mannooligosaccharides (MOS) after 34 h of fermentation did not significantly differ (69.76, 65.24 and 53.93%, respectively). At 24 h of fermentation, CMH promoted the growth of Lactobacillus and Bifidobacterium groups (P < 0.01) and did not significantly differ from the results obtained using FOS. The results of in vitro fecal fermentation of CMH indicate that CMH can promote the growth of beneficial bacteria.

Nondigestible carbohydrates, butyrate, and butyrate-producing bacteria

Nondigestible carbohydrates (NDCs) are fermentation substrates in the colon after escaping digestion in the upper gastrointestinal tract. Among NDCs, resistant starch is not hydrolyzed by pancreatic amylases but can be degraded by enzymes produced by large intestinal bacteria, including clostridia, bacteroides, and bifidobacteria. Nonstarch polysaccharides, such as pectin, guar gum, alginate, arabinoxylan, and inulin fructans, and nondigestible oligosaccharides and their derivatives, can also be fermented by beneficial bacteria in the large intestine. Butyrate is one of the most important metabolites produced through gastrointestinal microbial fermentation and functions as a major energy source for colonocytes by directly affecting the growth and differentiation of colonocytes. Moreover, butyrate has various physiological effects, including enhancement of intestinal barrier function and mucosal immunity. In this review, several representative NDCs are introduced, and their chemical components, structures, and physiological functions, including promotion of the proliferation of butyrate-producing bacteria and enhancement of butyrate production, are discussed. We also describe the strategies for achieving directional accumulation of colonic butyrate based on endogenous generation mechanisms.

Oral administration of antibiotics results in fecal occult bleeding due to metabolic disorders and defective proliferation of the gut epithelial cell in mice

Antibiotics sometimes exert adverse effects on the pathogenesis of colitis due to the dysbiosis resulting from the disruption of gut homeostasis. However, the precise mechanisms underlying colitogenic effects of antibiotic-induced colitis are largely unknown. Here, we show a novel murine fecal occult bleeding model induced by the combinatorial treatment of ampicillin and vancomycin, which is accompanied by an enlarged cecum, upregulation of pro-inflammatory cytokines IL-6 and IL-12, a reduction in Ki-67-positive epithelial cell number and an increase in the apoptotic cell number in the colon. Moreover, gas chromatography-tandem mass analysis showed that various kinds of metabolites, including glutamic acid and butyric acid, were significantly decreased in the cecal contents. In addition, abundance of butyric acid producer Clostridiales was dramatically reduced in the enlarged cecum. Interestingly, supplementation of monosodium glutamate or its precursor glutamine suppressed colonic IL-6 and IL-12, protected from cell apoptosis and prevented fecal occult blood indicating that the reduced level of glutamic acid is a possible mechanism of antibiotic-induced fecal occult bleeding. Our data showed a novel mechanism of antibiotic-induced fecal occult bleeding providing a new insight into the clinical application of glutamic acid for the treatment of antibiotic-induced colitis.

Cecal Microbiome Analyses on Wild Japanese Rock Ptarmigans (Lagopus muta japonica) Reveals High Level of Coexistence of Lactic Acid Bacteria and Lactate-Utilizing Bacteria

Preservation of indigenous gastrointestinal microbiota is critical for successful captive breeding of endangered wild animals, yet its biology is poorly understood. Here, we compared the cecal microbial composition of wild living Japanese rock ptarmigans (Lagopus muta japonica) in different locations of Japanese mountains, and the dominant cecal microbial structure of wild Japanese rock ptarmigans is elucidated. Coriobacteraceae and Lachnospraceae were the two dominant bacterial families in all samples analyzed. At the genus level, 10 genera Olsenella, Actinomyces, Megasphaera, Slackia, Cloacibacillus, Bifidobacterium,Escherichia,Dialister, Megamonas, and Bilophila were dominant. These results reveal the high level of coexistence of lactic acid bacteria (Olsenella and Bifidobacterium) and lactate-utilizing bacteria (Megasphaera). This coexistence should be taken into account for the successful breeding of captive Japanese rock ptarmigans in the national conservation program.

Dietary Clostridium butyricum Induces a Phased Shift in Fecal Microbiota Structure and Increases the Acetic Acid-Producing Bacteria in a Weaned Piglet Model

Clostridium butyricum is known as a butyrate producer and a regulator of gut health, but whether it exerts a beneficial effect as a dietary supplement via modulating the intestinal microbiota remains elusive. This study investigated the impact of C. butyricum on the fecal microbiota composition and their metabolites 14 and 28 days after weaning with 10 g/kg dietary supplementation of C. butyricum. Dynamic changes of microbial compositions showed dramatically increasing Selenomonadales and decreasing Clostridiales on days 14 and 28. Within Selenomonadales, Megasphaera became the main responder by increasing from 3.79 to 11.31%. Following the prevalence of some acetate producers ( Magasphaera) and utilizers ( Eubacterium_hallii) at the genus level and even with a significant decrease in fecal acetate on day 28, the present data suggested that C. butyricum influenced microbial metabolism by optimizing the structure of microbiota and enhancing acetate production and utilization for butyrate production.

In vitro fermentation of copra meal hydrolysate by chicken microbiota

The aim of this study was to carry out preliminary investigations on the in vitro fermentation selectivity of copra meal hydrolysate (CMH) by chicken gut microbiota. The ileum and cecum contents from three 35-day-old birds were used as inocula. Yeast mannooligosaccharide (yeast-MOS) or α-mannan was selected as a positive control. Batch culture fermentation with fecal bacteria was performed at 42 °C for 24 h in an anaerobic chamber. Samples were collected at 0, 6, 12, 18 and 24 h of fermentation and evaluated using real-time PCR and short-chain fatty acid (SCFA) analysis. Results showed that the medium containing ileum and both CMH and yeast-MOS substrates led to an increase in the growth of the dominant groups as Lactobacillus, Enterobacteriaceae and Enterococcus spp. compared with 0-h fermentation. Campylobacter spp. and Bifidobacterium spp. were not detected in any samples. A significant decrease in Acinetobacter was observed in all substrates tested after 6 h of fermentation (P < 0.05). Only the sample from CMH fermentation showed a significantly greater reduction in the population of Pseudomonas after 18-h fermentation with ileum content (P < 0.05). Propionate was the main fermentation product found in both ileum and cecum fermentation followed by lactate and acetate. CMH can be utilized by ileum and cecum microbial of chickens, and CMH has a generally desirable effect on the microbiota. CMH has the potential for use as a supplementary diet with similar or improved benefits and lower costs compared to commercial prebiotics. Further experiments in animal trials would seem to be justified.

The effect of storage at ambient temperature on the feline fecal microbiota

BACKGROUND

Feline fecal microbiota analyses can potentially be impacted by a variety of factors such as sample preparation, sequencing method and bioinformatics analyses. Another potential influence is changes in the microbiota from storage of samples prior to processing. This study examined the effect of ambient temperature exposure on the feline fecal microbiota composition. Fecal samples were collected from 12 healthy cats, within 15 min after defecation. Samples were aliquoted and the first aliquot was frozen at -80 °C within 1 hour of defecation. Remaining aliquots were maintained at ambient temperature (20 to 23 °C) and frozen at -80 °C at 6, 12, 24, 36, 48, 72 and 96 h after collection. DNA was extracted from all aliquots, and polymerase chain reaction (PCR). The PCR products were sequenced with next-generation sequencing (Illumina MiSeq).

RESULTS

No significant differences were observed in alpha and beta biodiversity indexes, as well as relative abundance of different taxa over time (P > 0.05 for all tests between time points). Principal coordinate analyses demonstrated that samples cluster mainly by cat, with no significant differences between time points (AMOVA, P > 0.05; HOMOVA, P > 0.05). Linear discriminant analysis effect size method was performed and failed to detect any enriched taxa, between time points. Random forest algorithm analysis indicated homogeneity across time points.

CONCLUSIONS

Although existing evidence from human fecal storage studies is contradictory, a recent study in companion animals agreed with the current study, demonstrating that maintenance of feline fecal samples at ambient temperature for up to 4 days has no effect on the bacterial membership and structure.

Microbial shifts in the porcine distal gut in response to diets supplemented with Enterococcus Faecalis as alternatives to antibiotics

Gut microbiota plays an important role in host health and nutrient digestion of animals. Probiotics have become one of effective alternatives to antibiotics enhancing animal health and performance through modulating gut microbiota. Previously, our research demonstrated that dietary Enterococcus Faecalis UC-100 substituting antibiotics enhanced growth and health of weaned pigs. To investigate the alterations of microbiota in the distal gut of pigs fed E. faecalis UC-100 substituting antibiotics, this study assessed fecal microbiota in pigs from different dietary treatments: the basal diet group, the E. faecalis group, and the antibiotic group on d 0, 14, and 28 of feeding through 16 S rRNA sequencing. Twenty-one phyla and 137 genera were shared by all pigs, whereas 12 genera were uniquely identified in the E. faecalis group on d 14 and 28. Bacterial abundance and diversity in the E. faecalis group, bacterial diversity in the antibiotic group, especially abundances of Fibrobacteres phylum and 12 genera in the E. faecalis group and antibiotics group were lower than that in the basal diet group on d 28. These results showed that microbial shifts in the porcine gut in response to diets containing E. faecalis were similar to the response to which containing antibiotics.

Gut microbial metabolism defines host metabolism: an emerging perspective in obesity and allergic inflammation

The presence of >100 trillion microorganisms (collectively called gut microbiota) in our large intestine is essential for the maintenance of health. The gut microbiota starts to develop before birth and matures within first three years of life. The Western diet and lifestyle have been implicated in causing an imbalance of gut microbial communities and their metabolites that consequence in disease states, such as obesity and asthma. With more than 13% of the world population currently living with obesity and one out of 10 children diagnosed with asthma, we explore here the recent developments in the biosynthesis and mode of action of the key metabolites in relation to these two chronic inflammatory conditions.

A Longitudinal Study of the Feline Faecal Microbiome Identifies Changes into Early Adulthood Irrespective of Sexual Development

Companion animals provide an excellent model for studies of the gut microbiome because potential confounders such as diet and environment can be more readily controlled for than in humans. Additionally, domestic cats and dogs are typically neutered early in life, enabling an investigation into the potential effect of sex hormones on the microbiome. In a longitudinal study to investigate the potential effects of neutering, neutering age and gender on the gut microbiome during growth, the faeces of kittens (16 male, 14 female) were sampled at 18, 30 and 42 weeks of age. DNA was shotgun sequenced on the Illumina platform and sequence reads were annotated for taxonomy and function by comparison to a database of protein coding genes. In a statistical analysis of diversity, taxonomy and functional potential of the microbiomes, age was identified as the only factor with significant associations. No significant effects were detected for gender, neutering, or age when neutered (19 or 31 weeks). At 18 weeks of age the microbiome was dominated by the genera Lactobacillus and Bifidobacterium (35% and 20% average abundance). Structural and functional diversity was significantly increased by week 30 but there was no further significant increase. At 42 weeks of age the most abundant genera were Bacteroides (16%), Prevotella (14%) and Megasphaera (8%). Significant differences in functional potential included an enrichment for genes in energy metabolism (carbon metabolism and oxidative phosphorylation) and depletion in cell motility (flagella and chemotaxis). We conclude that the feline faecal microbiome is predominantly determined by age when diet and environment are controlled for. We suggest this finding may also be informative for studies of the human microbiome, where control over such factors is usually limited.

Alterations in the Colonic Microbiota of Pigs Associated with Feeding Distillers Dried Grains with Solubles

In an effort to reduce feed costs, many pork producers have increased their use of coproducts of biofuel production in commercial pig diets, including increased feeding of distiller's dried grains with solubles (DDGS). The inclusion of DDGS increases the insoluble fiber content in the ration, which has the potential to impact the colonic microbiota considerably as the large intestine contains a dynamic microenvironment with tremendous interplay between microorganisms. Any alteration to the physical or chemical properties of the colonic contents has the potential to impact the resident bacterial population and potentially favor or inhibit the establishment of pathogenic species. In the present study, colonic contents collected at necropsy from pigs fed either 30% or no DDGS were analyzed to examine the relative abundance of bacterial taxa associated with feeding this ingredient. No difference in alpha diversity (richness) was detected between diet groups. However, the beta diversity was significantly different between groups with feeding of DDGS being associated with a decreased Firmicutes:Bacteriodetes ratio (P = .004) and a significantly lower abundance of Lactobacillus spp. (P = .016). Predictive functional profiling of the microbiota revealed more predicted genes associated with carbohydrate metabolism, protein digestion, and degradation of glycans in the microbiota of pigs fed DDGS. Taken together, these findings confirm that alterations in dietary insoluble fiber significantly alter the colonic microbial profile of pigs and suggest the resultant microbiome may predispose to the development of colitis.

Deep Illumina-based shotgun sequencing reveals dietary effects on the structure and function of the fecal microbiome of growing kittens

Background

Previously, we demonstrated that dietary protein:carbohydrate ratio dramatically affects the fecal microbial taxonomic structure of kittens using targeted 16S gene sequencing. The present study, using the same fecal samples, applied deep Illumina shotgun sequencing to identify the diet-associated functional potential and analyze taxonomic changes of the feline fecal microbiome.

Methodology & Principal Findings

Fecal samples from kittens fed one of two diets differing in protein and carbohydrate content (high–protein, low–carbohydrate, HPLC; and moderate-protein, moderate-carbohydrate, MPMC) were collected at 8, 12 and 16 weeks of age (n = 6 per group). A total of 345.3 gigabases of sequence were generated from 36 samples, with 99.75% of annotated sequences identified as bacterial. At the genus level, 26% and 39% of reads were annotated for HPLC- and MPMC-fed kittens, with HPLC-fed cats showing greater species richness and microbial diversity. Two phyla, ten families and fifteen genera were responsible for more than 80% of the sequences at each taxonomic level for both diet groups, consistent with the previous taxonomic study. Significantly different abundances between diet groups were observed for 324 genera (56% of all genera identified) demonstrating widespread diet-induced changes in microbial taxonomic structure. Diversity was not affected over time. Functional analysis identified 2,013 putative enzyme function groups were different (p<0.000007) between the two dietary groups and were associated to 194 pathways, which formed five discrete clusters based on average relative abundance. Of those, ten contained more (p<0.022) enzyme functions with significant diet effects than expected by chance. Six pathways were related to amino acid biosynthesis and metabolism linking changes in dietary protein with functional differences of the gut microbiome.

Conclusions

These data indicate that feline feces-derived microbiomes have large structural and functional differences relating to the dietary protein:carbohydrate ratio and highlight the impact of diet early in life.

Expression of heat shock proteins 27 and 72 correlates with specific commensal microbes in different regions of porcine gastrointestinal tract

The gastrointestinal (GI) tract of mammals is inhabited by trillions of microorganisms, resulting in exceedingly complex networking. The interaction between distinct bacterial species and the host immune system is essential in maintaining homeostasis in the gut ecosystem. For instance, the gut commensal microbiota dictates intestinal mucosa maturation and its abundant immune components, such as cytoprotective heat shock proteins (HSP). Here we examined physiological expression of HSP in the normal porcine GI tract and found it to be gut region- and cell type-specific in response to dietary components, microbes, and microbial metabolites to which the mucosa surface is exposed. Correlations between HSP72 expression and ileal Lactobacillus spp. and colonic clostridia species, and between HSP27 expression and uronic acid ingestion, were important interplays identified here. Thus this study provides novel insights into host-microbe interactions shaping the immune system that are modifiable by dietary regime.

Megasphaera indica sp. nov., an obligate anaerobic bacteria isolated from human faeces

Two coccoid, non-motile, obligately anaerobic, Gram-stain-negative bacteria, occurring singly or in pairs, or as short chains, with a mean size of 1.4-2.5 µm were isolated from the faeces of two healthy human volunteers, aged 26 and 56 years, and were designated NMBHI-10(T) and BLPYG-7, respectively. Both the strains were affiliated to the sub-branch Sporomusa of the class Clostridia as revealed by 16S rRNA gene sequence analysis. The isolates NMBHI-10(T) and BLPYG-7 showed 99.1 and 99.2% 16S rRNA gene sequence similarity, respectively, with Megasphaera elsdenii JCM 1772(T). DNA-DNA hybridization and phenotypic analysis showed that both the strains were distinct from their closest relative, M. elsdenii JCM 1772(T) (42 and 53% DNA-DNA relatedness with NMBHI-10(T) and BLPYG-7, respectively), but belong to the same species (DNA-DNA relatedness of 80.9 % between the isolates). According to DNA-DNA hybridization results, the coccoid strains belong to the same genospecies, and neither is related to any of the recognized species of the genus Megasphaera. Strains NMBHI-10(T) and BLPYG-7 grew in PYG broth at temperatures of between 15 and 40 °C (optimum 37 °C), but not at 45 °C. The strains utilized a range of carbohydrates as sources of carbon and energy including glucose, lactose, cellobiose, rhamnose, galactose and sucrose. Glucose fermentation resulted in the formation of volatile fatty acids, mainly caproic acid and organic acids such as succinic acid. Phylogenetic analysis, specific phenotypic characteristics and/or DNA G+C content also differentiated the strains from each other and from their closest relatives. The DNA G+C contents of strains NMBHI-10(T) and BLPYG-7 are 57.7 and 54.9 mol%, respectively. The major fatty acids were 12 : 0 FAME and 17 : 0 CYC FAME. On the basis of these data, we conclude that strains NMBHI-10(T) and BLPYG-7 should be classified as representing a novel species of the genus Megasphaera, for which the name Megsphaera indica sp. nov. is proposed. The type strain is NMBHI-10(T) ( = DSM 25563(T) = MCC 2481(T)).

Heat Shock Proteins: Intestinal Gatekeepers that Are Influenced by Dietary Components and the Gut Microbiota

Trillions of microorganisms that inhabit the intestinal tract form a diverse and intricate ecosystem with a deeply embedded symbiotic relationship with their hosts. As more detailed information on gut microbiota complexity and functional diversity accumulates, we are learning more about how diet-microbiota interactions can influence the immune system within and outside the gut and host health in general. Heat shock proteins are a set of highly conserved proteins that are present in all types of cells, from microbes to mammals. These proteins carry out crucial intracellular housekeeping functions and unexpected extracellular immuno-regulatory features in order to maintain the mucosal barrier integrity and gut homeostasis. It is becoming evident that the enteric microbiota is one of the major determinants of heat shock protein production in intestinal epithelial cells. This review will focus on the interactions between diet, gut microbiota and their role for regulating heat shock protein production and, furthermore, how these interactions influence the immune system and the integrity of the mucosal barrier.

Impact of subacute ruminal acidosis on the diversity of liquid and solid-associated bacteria in the rumen of goats

This study was aimed to investigate the impact of subacute ruminal acidosis (SARA) on the diversity of liquid (LAB) and solid-associated bacteria (SAB) following high-grain feeding. Six ruminally cannulated goats were divided into two groups: one group was fed a hay diet (COD), and the other group was fed a high grain diet (SAID). Rumen liquids and rumen solids were sampled after 2 weeks adaption. SARA was diagnosed with a pH below 5.8 for 8 h. SAID decreased ruminal pH (P < 0.001) and increased the acetate (P = 0.017), propionate (P = 0.001), butyrate (P < 0.001) and total volatile fatty acid (P < 0.001) concentration in rumen compared with the COD. Denaturing gradient gel electrophoresis fingerprints analysis revealed a clear separation between both the diet and the fraction of rumen digesta in bacterial communities. Pyrosequencing analysis showed that the proportion of phylum Bacteroidetes in the SAID-LAB and SAID-SAB communities was less than in the COD group, whereas the SAID group had a greater percentage of Firmicutes in both the LAB and SAB libraries. UniFrac analyses and a Venn diagram revealed a large difference between the two diets in the diversity of rumen bacterial communities. Overall, our findings revealed that SARA feeding did alter the community structure of rumen liquids and rumen solids. Thus, manipulation of dietary factors, such as ratio of forage to concentrate may have the potential to alter the microbial composition of rumen liquid and rumen solid.

Intestinal colonization: how key microbial players become established in this dynamic process: microbial metabolic activities and the interplay between the host and microbes

In this review, we provide an overview of the dynamic changes within the microbiota and its metabolites that are implicated in establishing and maintaining gastrointestinal homeostasis during various stages of microbial colonization. The gradual conversion of the gut microbiota toward a mutualistic microbial community involves replacement of pioneer gut colonizers with bacterial taxa that are characteristic for the adult gut. An important microbial signature of homeostasis in the adult gut is the prevalence and activity of a diverse spectrum of bacterial species that produce beneficial metabolites through metabolic interactions between microbial groups. Deciphering these microbial signatures and their metabolites that govern short and long-term equilibrium, as well as imbalances in host-microbial relationships, may provide novel diagnostic tools and/or therapeutic targets for specific disorders associated with intestinal dysbiosis and loss of homeostasis.