Quantification of Bifidobacterium spp. and Lactobacillus spp. in rat fecal samples by real-time PCR

Comparison of gut microbiota profiles between patients suffering from elderly frailty syndrome and non-frail elderly individuals

BACKGROUND

Frailty syndrome is a state of increased vulnerability to stressors, marked by lowered physical strength and increased dependence on others. The well-established changes in gut microbiota associated with old age suggest a probable relationship between gut microbiota and frailty.

METHODS AND RESULTS

This study was aimed at finding the relationship between gut microbiota and frailty syndrome, by comparing the sociodemographic data and the gut microbiota profiles of 23 non-frail and 14 frail elderly individuals. We used the quantitative polymerase chain reaction method (qPCR) to determine the bacterial loads of Bifidobacteria, Lactobacillus, Bacteroidetes, Prevotella, and Escherichia coli in stool samples from test subjects. We discovered a significant increase in the bacterial load of Prevotella in frail elderly individuals aged 70 or above. Other bacterial loads and ratios were not significantly different between the two groups.

CONCLUSIONS

More comprehensive studies with larger sample sizes and encompassing a wider range of inflammation-related bacteria need to be performed to discover the existence and exact nature of these relations.

Effect of Blueberry Supplementation on a Diet-Induced Rat Model of Prediabetes-Focus on Hepatic Lipid Deposition, Endoplasmic Stress Response and Autophagy

Blueberries, red fruits enriched in polyphenols and fibers, are envisaged as a promising nutraceutical intervention in a plethora of metabolic diseases. Prediabetes, an intermediate state between normal glucose tolerance and type 2 diabetes, fuels the development of complications, including hepatic steatosis. In previous work, we have demonstrated that blueberry juice (BJ) supplementation benefits glycemic control and lipid profile, which was accompanied by an amelioration of hepatic mitochondrial bioenergetics. The purpose of this study is to clarify the impact of long-term BJ nutraceutical intervention on cellular mechanisms that govern hepatic lipid homeostasis, namely autophagy and endoplasmic reticulum (ER) stress, in a rat model of prediabetes. Two groups of male Wistar rats, 8-weeks old, were fed a prediabetes-inducing high-fat diet (HFD) and one group was fed a control diet (CD). From the timepoint where the prediabetic phenotype was achieved (week 16) until the end of the study (week 24), one of the HFD-fed groups was daily orally supplemented with 25 g/kg body weight (BW) of BJ (HFD + BJ). BW, caloric intake, glucose tolerance and insulin sensitivity were monitored throughout the study. The serum and hepatic lipid contents were quantified. Liver and interscapular brown and epidydimal white adipose tissue depots (iBAT and eWAT) were collected for histological analysis and to assess thermogenesis, ER stress and autophagy markers. The gut microbiota composition and the short-chain fatty acids (SCFAs) content were determined in colon fecal samples. BJ supplementation positively impacted glycemic control but was unable to prevent obesity and adiposity. BJ-treated animals presented a reduction in fecal SCFAs, increased markers of arrested iBAT thermogenesis and energy expenditure, together with an aggravation of HFD-induced lipotoxicity and hepatic steatosis, which were accompanied by the inhibition of autophagy and ER stress responses in the liver. In conclusion, despite the improvement of glucose tolerance, BJ supplementation promoted a major impact on lipid management mechanisms at liver and AT levels in prediabetic animals, which might affect disease course.

Rat microbial biogeography and age-dependent lactic acid bacteria in healthy lungs

The laboratory rat emerges as a useful tool for studying the interaction between the host and its microbiome. To advance principles relevant to the human microbiome, we systematically investigated and defined the multitissue microbial biogeography of healthy Fischer 344 rats across their lifespan. Microbial community profiling data were extracted and integrated with host transcriptomic data from the Sequencing Quality Control consortium. Unsupervised machine learning, correlation, taxonomic diversity and abundance analyses were performed to determine and characterize the rat microbial biogeography and identify four intertissue microbial heterogeneity patterns (P1-P4). We found that the 11 body habitats harbored a greater diversity of microbes than previously suspected. Lactic acid bacteria (LAB) abundance progressively declined in lungs from breastfed newborn to adolescence/adult, and was below detectable levels in elderly rats. Bioinformatics analyses indicate that the abundance of LAB may be modulated by the lung-immune axis. The presence and levels of LAB in lungs were further evaluated by PCR in two validation datasets. The lung, testes, thymus, kidney, adrenal and muscle niches were found to have age-dependent alterations in microbial abundance. The 357 microbial signatures were positively correlated with host genes in cell proliferation (P1), DNA damage repair (P2) and DNA transcription (P3). Our study established a link between the metabolic properties of LAB with lung microbiota maturation and development. Breastfeeding and environmental exposure influence microbiome composition and host health and longevity. The inferred rat microbial biogeography and pattern-specific microbial signatures could be useful for microbiome therapeutic approaches to human health and life quality enhancement.

Effects of the combination of Lactobacillus helveticus and isomalto-oligosaccharide on survival, gut microbiota, and immune function in Apis cerana worker bees

The adult worker bees were fed sucrose syrup or sucrose syrup supplemented with Lactobacillus helveticus KM7, prebiotic isomalto-oligosaccharide (IMO), or L. helveticus KM7 combined with IMO. Survival rate, gut microbiota, and gene expression of gut antimicrobial peptides in worker honey bees were determined. Administration of L. helveticus KM7 and IMO significantly increased the survival rate in worker bees relative to bees fed sucrose only. Then, higher concentration of both lactic acid bacteria and Bifidobacterium in the gut and lower counts of gut fungi, Enterococcus, and Bacteroides-Porphyromonas-Prevotella were observed in bees fed the combination of KM7 and IMO compared with control bees. The combination of L. helveticus KM7 with IMO showed a greater or comparable modulating effect on those bacteria relative to either KM7 or IMO alone. Furthermore, the combination treatment of L. helveticus KM7 and IMO enhanced mRNA expression of antimicrobial peptide genes, including Abaecin, Defensin, and the gene encoding prophenoloxidase (PPO) in the gut compared with both control bees and those either L. helveticus KM7 or IMO alone. These results suggest that the combination of L. helveticus KM7 and IMO synergistically modifies the gut microbiota and immunity and consequently improves the survival rate of Apis cerana adult workers.

Genome-wide mapping of gene-microbe interactions in the murine lung microbiota based on quantitative microbial profiling

BACKGROUND

Mammalian lungs comprise a complex microbial ecosystem that interacts with host physiology. Previous research demonstrates that the environment significantly contributes to bacterial community structure in the upper and lower respiratory tract. However, the influence of host genetics on the makeup of lung microbiota remains ambiguous, largely due to technical difficulties related to sampling, as well as challenges inherent to investigating low biomass communities. Thus, innovative approaches are warranted to clarify host-microbe interactions in the mammalian lung.

RESULTS

Here, we aimed to characterize host genomic regions associated with lung bacterial traits in an advanced intercross mouse line (AIL). By performing quantitative microbial profiling (QMP) using the highly precise method of droplet digital PCR (ddPCR), we refined 16S rRNA gene amplicon-based traits to identify and map candidate lung-resident taxa using a QTL mapping approach. In addition, the two abundant core taxa Lactobacillus and Pelomonas were chosen for independent microbial phenotyping using genus-specific primers. In total, this revealed seven significant loci involving eight bacterial traits. The narrow confidence intervals afforded by the AIL population allowed us to identify several promising candidate genes related to immune and inflammatory responses, cell apoptosis, DNA repair, and lung functioning and disease susceptibility. Interestingly, one genomic region associated with Lactobacillus abundance contains the well-known anti-inflammatory cytokine Il10, which we confirmed through the analysis of Il10 knockout mice.

CONCLUSIONS

Our study provides the first evidence for a role of host genetic variation contributing to variation in the lung microbiota. This was in large part made possible through the careful curation of 16S rRNA gene amplicon data and the incorporation of a QMP-based methods. This approach to evaluating the low biomass lung environment opens new avenues for advancing lung microbiome research using animal models.

Rat microbial biogeography and age-dependent lactic acid bacteria in healthy lungs

The laboratory rat emerges as a useful tool for studying the interaction between the host and its microbiome. To advance principles relevant to the human microbiome, we systematically investigated and defined a multi-tissue full lifespan microbial biogeography for healthy Fischer 344 rats. Microbial community profiling data was extracted and integrated with host transcriptomic data from the Sequencing Quality Control (SEQC) consortium. Unsupervised machine learning, Spearman's correlation, taxonomic diversity, and abundance analyses were performed to determine and characterize the rat microbial biogeography and the identification of four inter-tissue microbial heterogeneity patterns (P1-P4). The 11 body habitats harbor a greater diversity of microbes than previously suspected. Lactic acid bacteria (LAB) abundances progressively declined in lungs from breastfeed newborn to adolescence/adult and was below detectable levels in elderly rats. LAB's presence and levels in lungs were further evaluated by PCR in the two validation datasets. The lung, testes, thymus, kidney, adrenal, and muscle niches were found to have age-dependent alterations in microbial abundance. P1 is dominated by lung samples. P2 contains the largest sample size and is enriched for environmental species. Liver and muscle samples were mostly classified into P3. Archaea species were exclusively enriched in P4. The 357 pattern-specific microbial signatures were positively correlated with host genes in cell migration and proliferation (P1), DNA damage repair and synaptic transmissions (P2), as well as DNA transcription and cell cycle in P3. Our study established a link between metabolic properties of LAB with lung microbiota maturation and development. Breastfeeding and environmental exposure influence microbiome composition and host health and longevity. The inferred rat microbial biogeography and pattern-specific microbial signatures would be useful for microbiome therapeutic approaches to human health and good quality of life.

Lignin from sugarcane bagasse as a prebiotic additive for poultry feed

Diet is a crucial factor on health and well-being of livestock animals. Nutritional strengthening with diet formulations is essential to the livestock industry and animal perfor-mance. Searching for valuable feed additives among by-products may promote not only circular economy, but also functional diets. Lignin from sugarcane bagasse was proposed as a potential prebiotic additive for chickens and incorporated at 1 % (w/w) in commercial chicken feed, tested in two feed forms, namely, mash and pellets. Physico-chemical characterization of both feed types with and without lignin was performed. Also, the prebiotic potential for feeds with lignin was assessed by in vitro gastrointestinal model and evaluated the impact on chicken cecal Lactobacillus and Bifidobacterium. As for the pellet's physical quality, there was a higher cohesion of the pellets with lignin, indicating a higher resistance to breakout and lignin decreases the tendency of the pellets for microbial contamination. Regarding the prebiotic potential, mash feed with lignin showed higher promotion of Bifidobacterium in comparison with mash feed without lignin and to pellet feed with lignin. Lignin from sugarcane bagasse has prebiotic potential as additive to chicken feed when supplemented in mash feed diets, presenting itself as a sustainable and eco-friendly alternative to chicken feed additives supplementation.

Dietary and phytogenic inclusion effects on the broiler chicken cecal ecosystem

Dietary modulation in broilers is crucial for the establishment of beneficial microbiota and, subsequently, the promotion of intestinal health. In this trial, a 2 × 2 factorial design was used with two different specifications with respect to dietary metabolizable energy (ME) and crude protein (CP) levels (i.e., 95% and 100% of recommendations) and phytogenic levels (0 and 150 mg/kg). Levels of total bacteria, Bacteroides spp., Lactobacillus spp., and Clostridium cluster XIVa attached to the cecal mucosa and in the cecal digesta were lower in broilers fed the 95% ME and CP specification diets, as was the molar ratio of butyric acid. In addition, the relative activity of autoinducers-2 (AI-2) and the expression levels of TLR4 and AvBD6 were increased. Phytogenic supplementation reduced cecal digesta levels of Escherichia coli and Clostridium cluster I levels, and increased Clostridium cluster IV levels. Moreover, the butyric acid molar ratio and the relative activity of AI-2 were increased, whereas the concentration of branched VFAs and the expression of AvBD6 and LEAP2 were reduced by phytogenic administration. Dietary specifications and phytogenic interactions were shown for the cecal-attached microbiota composition, metabolic activity of digesta microbiota, relative expression of autoinducers-2, and relative expression of toll-like signaling molecules and host antimicrobial peptides. In conclusion, it has been shown that ME and CP dietary specifications, combined or not with phytogenics, modulate multilevel gut biomarkers ranging from microbiota composition and metabolic activity to microbial communications and host signaling, inflammation, and defense.

Effects of different processing techniques of palm kernel cake on processing quality of pellet feed, nutrient digestibility, and intestinal microbiota of pigs

The present study was conducted to investigate the effects of extrusion, fermentation, and enzymolysis of palm kernel cake on processing quality of pellet feed, nutrient digestibility, and intestinal microbiota of pigs. First, the pretreatment parameters of extrusion, enzymolysis, and fermentation of palm kernel cake were optimized. Then, PKC after three processing techniques were used to prepare pellet feed. A total of 160 crossbred piglets (Duroc × Landrace × Yorkshire) with an average body weight of 28 ± 0.5 kg were used in an 8-wk feeding experiment. Pigs were randomly assigned to five treatments with four replicates per treatment and eight pigs per replicates. The five experimental groups were as follows: basal diet group (whole corn-soybean meal), 10% PKC group (PKC), 10% extrusion PKC group (PPKC), 10% enzymolysis PKC group (EPKC), and 10% fermented PKC group (FPKC), respectively. At the end of the experiment, four pigs from each treatment (randomly collected one pig per pen) were sacrificed by administering a pentobarbital overdose, the gut and blood samples were collected for the quantification analysis of microbiota, hematological parameters, and apparent total tract nutrient digestibility. The results showed that all three processing techniques significantly decreased the contents of crude fiber of PKC (P < 0.01), pulverization rate (P < 0.01), powder content (P < 0.01), and increased the hardness and gelatinization starch of pellet feed (P < 0.05) compared to PKC group. In addition, PPKC significantly improved the dry matter, crude protein, and ether extract content, blood indices and average daily feed intake compared to PKC group (P < 0.01), while the parameters were similar among FPKC, EPKC, and control group (P > 0.01). Furthermore, all three processing techniques significantly increased the Lactobacillus and decreased the Escherichia levels in feces or gut compared to PKC. Collectively, extrusion, fermentation, and enzymolysis of PKC had positively enhanced the pellet quality, growth performance, nutrient digestibility, and gut microbiota, extrusion exhibited a superior feeding effect compared to fermentation and enzymolysis.

Bifidobacterium longum subsp. infantis utilizes human milk urea to recycle nitrogen within the infant gut microbiome

Human milk guides the structure and function of microbial commensal communities that colonize the nursing infant gut. Indigestible molecules dissolved in human milk establish a microbiome often dominated by bifidobacteria capable of utilizing these substrates. Interestingly, urea accounts for ~15% of total human milk nitrogen, representing a potential reservoir for microbiota that may be salvaged for critical metabolic operations during lactation and neonatal development. Accordingly, B. infantis strains are competent for urea nitrogen utilization, constituting a previously hypothetical phenotype in commensal bacteria hosted by humans. Urease gene expression, downstream nitrogen metabolic pathways, and enzymatic activity are induced during urea utilization to yield elevated ammonia concentrations. Moreover, biosynthetic networks relevant to infant nutrition and development are transcriptionally responsive to urea utilization including branched chain and other essential amino acids. Importantly, isotopically labeled urea nitrogen is broadly distributed throughout the expressed B. infantis proteome. This incisively demonstrates that the previously inaccessible urea nitrogen is incorporated into microbial products available for infant host utilization. In aggregate, B. infantis possesses the requisite phenotypic foundation to participate in human milk urea nitrogen recycling within its infant host and thus may be a key contributor to nitrogen homeostasis early in life.

Porcine spinal cord injury model for translational research across multiple functional systems

Animal models are necessary to identify pathological changes and help assess therapeutic outcomes following spinal cord injury (SCI). Small animal models offer value in research in terms of their easily managed size, minimal maintenance requirements, lower cost, well-characterized genomes, and ability to power research studies. However, despite these benefits, small animal models have neurologic and anatomical differences that may influence translation of results to humans and thus limiting the success of their use in preclinical studies as a direct pipeline to clinical studies. Large animal models, offer an attractive intermediary translation model that may be more successful in translating to the clinic for SCI research. This is largely due to their greater neurologic and anatomical similarities to humans. The physical characteristics of pig spinal cord, gut microbiome, metabolism, proportions of white to grey matter, bowel anatomy and function, and urinary system are strikingly similar and provide great insight into human SCI conditions. In this review, we address the variety of existing porcine injury models and their translational relevance, benefits, and drawbacks in modeling human systems and functions for neurophysiology, cardiovascular, gastrointestinal and urodynamic functions.

Probiotics and prebiotics alleviate behavioral deficits, inflammatory response, and gut dysbiosis in prenatal VPA-induced rodent model of autism

Autism spectrum disorders are neuropsychiatric conditions characterized by social interaction and communication disorders and repetitive stereotypical behaviors. These disorders are also accompanied by an inflammatory status. Bidirectional communication between microbiome, gut, and brain has been discovered as a major mechanism influencing core symptoms and biomarkers of autism. Therefore, the modulation of the gut microbiota in autism has recently attracted interest. In this study, probiotic- and prebiotic-mediated modulation of the gut microbiota was compared in terms of different symptoms and findings in an experimental autism model. Valproic acid (VPA) (500 mg/kg) was administered to Wistar rats (on prenatal day 12.5) to induce autistic-like behaviors. Based on the supply of probiotics and prebiotics, animals were grouped as control (saline), autistic-like (prenatal VPA), probiotic (prenatal VPA + 22.5 × 10⁹ cfu/day probiotic), prebiotic (prenatal VPA + 100 mg/day prebiotic), and combined treatment (prenatal VPA + 22.5 × 10⁹ cfu/day probiotic + 100 mg/day prebiotic). After the treatment process, behavioral tests (social behaviors, anxiety, stereotypical behavior, sensorimotor gating, and behavioral despair) and biochemical analyses (serum and brain tissue) were conducted, and the quantities of some phyla and genera were determined in stool samples. Significant positive effects of probiotic and combined treatments were observed on the sociability, social interaction, and anxiety parameters. In addition, all three treatments had positive effects on stereotypical behavior. However, the treatments did not affect sensorimotor gating deficits and behavioral despair. Further, probiotic treatment reversed the VPA-induced increase and decrease in serum IL-6 and IL-10 levels, respectively. Combined treatment also significantly increased the IL-10 levels. Prenatal VPA exposure decreased 5-hydroxytryptamine (5-HT) levels in the prefrontal cortex of the brain; however, combined treatment reversed this decrease. Prenatal VPA exposure also caused a decrease in Bacteroidetes/Firmicutes ratio in the gut microbiota, while the probiotic treatment significantly increased this ratio. These findings indicate that probiotic- and prebiotic-mediated microbial modulation may represent a new therapeutic approach to alleviate autistic-like symptoms.

Multi-omics analyses of airway host-microbe interactions in chronic obstructive pulmonary disease identify potential therapeutic interventions

The mechanistic role of the airway microbiome in chronic obstructive pulmonary disease (COPD) remains largely unexplored. We present a landscape of airway microbe-host interactions in COPD through an in-depth profiling of the sputum metagenome, metabolome, host transcriptome and proteome from 99 patients with COPD and 36 healthy individuals in China. Multi-omics data were integrated using sequential mediation analysis, to assess in silico associations of the microbiome with two primary COPD inflammatory endotypes, neutrophilic or eosinophilic inflammation, mediated through microbial metabolic interaction with host gene expression. Hypotheses of microbiome-metabolite-host interaction were identified by leveraging microbial genetic information and established metabolite-human gene pairs. A prominent hypothesis for neutrophil-predominant COPD was altered tryptophan metabolism in airway lactobacilli associated with reduced indole-3-acetic acid (IAA), which was in turn linked to perturbed host interleukin-22 signalling and epithelial cell apoptosis pathways. In vivo and in vitro studies showed that airway microbiome-derived IAA mitigates neutrophilic inflammation, apoptosis, emphysema and lung function decline, via macrophage-epithelial cell cross-talk mediated by interleukin-22. Intranasal inoculation of two airway lactobacilli restored IAA and recapitulated its protective effects in mice. These findings provide the rationale for therapeutically targeting microbe-host interaction in COPD.

Physical activity enhances fecal lactobacilli in rats chronically drinking sweetened cola beverage

Overweight and obesity have been linked with increased intake of sugar-sweetened beverages. On the other hand, physical activity has been known to lead to weight loss. Therefore, we hypothesized that exercise might influence the Lactobacillus population in fecal microbiota as their changed abundance is often associated with shifts in the physical activity and diet. In our experiment, Wistar rats were allocated into groups with normal feed or added sugar-sweetened beverages with or without access to a running wheel. Interestingly, only a combination of physical activity and sweetened beverage intake was associated with a significant increase in fecal lactobacilli abundance, suggesting a connection between exercise and a rise in lactobacilli abundance. Moreover, physical activity has improved weight-related parameters and led to increased plasma and mRNA adiponectin levels. Ghrelin and leptin plasma levels were unaltered. Taken together, our results demonstrate that effect of physical activity on adiposity even during unhealthy feeding patterns is accompanied by increased lactobacilli abundance in the fecal microbiota population.

Correlation of Gut Microbiota, Vitamin D Status, and Pulmonary Function Tests in Children With Cystic Fibrosis

Background

Children with cystic fibrosis (CF) are expected to have suboptimal serum vitamin D status and altered gut microbiota. The altered gut microbiota is hypothesized to have a pro-inflammatory effect that further complicates the existing respiratory inflammation. Emerging evidence suggests an association between vitamin D and gut microbiota. The aim of this study was to assess the relationships between 25-hydroxyvitamin D [25(OH)D] status, pulmonary function, and fecal bacteria in children with CF.

Methods

In this cross-sectional study, a total of 35 children with CF (8.7 ± 2.83 years) and 24 controls without CF (9 ± 2.7 years) were included in this study. Serum 25(OH)D status was measured using the Elecsys vitamin D total II assay. In the CF group, gut microbiota composition was assessed using real-time PCR analysis. Pulmonary function tests (PFTs) were measured using spirometry. Comparisons between the CF and non-CF controls were conducted using the independent sample t-test. In the CF group, one-way analysis of variance (ANOVA) was used to assess differences in PFTs and gut microbiota composition across the three vitamin D subgroups. The correlations between 25(OH)D status and PFTs, or gut microbiota composition, and PFTs with gut microbiota composition were analyzed using the Pearson's correlation coefficient test.

Results

Children with CF had significantly lower serum 25(OH)D levels compared with children without CF (44.3 ± 22.4 vs. 59 ± 25.5, respectively, P = 0.026). Children with CF with optimal serum 25(OH)D level had significantly higher levels of Bacteroidetes, Firmicutes, and total bacteria (P = 0.007, P = 0.007, and P = 0.022, respectively). The level of Firmicutes was found to be significantly higher in mild forced expiratory volume in 1 s (FEV1) compared with moderate FEV1 (P = 0.032), whereas the level of the other bacteria species was comparable across FEV1 severity groups.

Conclusion

Our findings may encourage studies that target and modify gut microbiota to potentially achieve better outcomes in terms of respiratory function in CF.

Effect of daily co-exposure to inulin and chlorpyrifos on selected microbiota endpoints in the SHIME® model

The intestinal microbiota has a key role in human health via the interaction with the somatic and immune cells in the digestive tract environment. Food, through matrix effect, nutrient and non-nutrient molecules, is a key regulator of microbiota diversity. As a food contaminant, the pesticide chlorpyrifos (CPF) has an effect on the composition of the intestinal microbiota and induces perturbation of microbiota. Prebiotics (and notably inulin) are known for their ability to promote an equilibrium of the microbiota that favours saccharolytic bacteria. The SHIME® dynamic in vitro model of the human intestine was exposed to CPF and inulin concomitantly for 30 days, in order to assess variations in both the bacterial populations and their metabolites. Various analyses of the microbiota (notably temporal temperature gradient gel electrophoresis) revealed a protective effect of the prebiotic through inhibition of the enterobacterial (E. coli) population. Bifidobacteria were only temporarily inhibited at D15 and recovered at D30. Although other potentially beneficial populations (lactobacilli) were not greatly modified, their activity and that of the saccharolytic bacteria in general were highlighted by an increase in levels of short-chain fatty acids and more specifically butyrate. Given the known role of host-microbiota communication, CPF's impact on the body's homeostasis remains to be determined.

Antiobesity, Antihyperglycemic, and Antidepressive Potentiality of Rice Fermented Food Through Modulation of Intestinal Microbiota

The present study has been aimed at evaluating the antiobesity, antihyperglycemic, and antidepressive potentials of Asparagus racemosus starter-based rice fermented foods. High-throughput NGS technology has revealed a number of bacterial genera in the prepared fermented rice, such as Lactobacillus (29.44%), Brevundimonas (16.21%), Stenotrophomonas (6.18%), Pseudomonas (3.11%), Bacillus (2.88%), and others (<2%). Eight-week administration of rice fermented food has increased food intake, whole-body weight, organ weight, different fat masses, serum lipid profiles, and histology of liver and adipose tissues in HFD-induced obese mice. In addition, upregulation of fatty acid oxidation and downregulation of adipocytogenesis- and lypogenesis-related genes along with the expression of their regulatory nuclear factors such as PPARα, PPARγ, PPARδ, and SREBP-1c have also been noted. Moreover, fermented food decreases fasting blood glucose level and improves glucose and insulin tolerance as well as the expression of GLUT4 receptor. Antiobesity and antihyperglycemic effects are also supported by the changes in insulin, leptin, and adiponectin hormone levels. The real-time polymerase chain reaction (RT-PCR) and denaturing gradient gel electrophoresis (DGGE) analyses have clearly demonstrated the intense colonization of Bacteroides, Lactobacillus, and Bifidobacterium, as well as the suppressed growth rate of γ- and δ-Proteobacteria and Firmicutes in the gut after fermented food intake. In the intestine, the latter group of microorganisms possibly modulate short-chain fatty acid (SCFA) levels such as acetate, butyrate, and propionate more than twofold. The impairment of memory-learning and anxiety-like obesity-associated cognitive phenotypes is mitigated significantly (p < 0.01) by fermented food as well. Thus, the formulated fermented food could be used as a natural therapeutic to alleviate obesity and its associated psychological and pathophysiological ailments.

Determinants of Leaky Gut and Gut Microbiota Differences in Children With Autism Spectrum Disorder and Their Siblings

Leaky gut hypothesis is one of the well-known theory which tries to explain etiology of Autism Spectrum Disorder (ASD). Unfortunately there is still a gap of evidence to investigate the corner points of the hypothesis. The aim of this study was to investigate the determinants of leaky gut in children with ASD, their siblings and healthy controls. Intestinal microbiota was found to be similar between ASD and sibling groups. Biological markers of bacterial translocation showed a significant difference in the sibling group, whereas the marker indicating local inflammation was not different between the groups. The findings from this study did not support the role of Gut microbiota or leaky gut on the etiology of autism.

Can Supplemented Skim Milk (SKM) Boost Your Gut Health?

The incorporation of functional ingredients, such as prebiotics and probiotics in food matrices, became a common practice in the human diet to improve the nutritional value of the food product itself. Worldwide, skim milk (SKM) is one of the most consumed food matrices, comprising all the essential nutrients desired for a balanced diet. Thus, the modulation of the human gut microbiota by SKM supplemented with different well-known functional ingredients was evaluated. Four well-studied prebiotics, fructo-oligosaccharides (FOS), galacto-oligosaccharides (GOS), mannan-oligosaccharides (MOS) and inulin, and one probiotic product, UL-250® (Saccharomyces boulardii) were added at 1% (w/v) to SKM and subjected to a gastrointestinal in vitro model. The impact of each combination on gut microbiota profile and their fermentation metabolites (i.e., short-chain fatty acids–SCFA) was assessed by quantitative polymerase chain reaction (qPCR) and high-performance liquid chromatography (HPLC), respectively. The addition of FOS to SKM had promising results, showing prebiotic potential by promoting the growth of Lactobacillus, Bifidobacterium, and Clostridium cluster IV. Moreover, the increment of SCFA levels and the decrease of total ammonia nitrogen were observed throughout colonic fermentation. Overall, these results demonstrate that the combination SKM + FOS was the most beneficial to the host’s health by positively modulating the gut microbiota.

Cell factory for γ-aminobutyric acid (GABA) production using Bifidobacterium adolescentis

Background

Bifidobacteria are gram-positive, probiotic, and generally regarded as safe bacteria. Techniques such as transformation, gene knockout, and heterologous gene expression have been established for Bifidobacterium, indicating that this bacterium can be used as a cell factory platform. However, there are limited previous reports in this field, likely because of factors such as the highly anaerobic nature of this bacterium. Bifidobacterium adolescentis is among the most oxygen-sensitive Bifidobacterium species. It shows strain-specific gamma-aminobutyric acid (GABA) production. GABA is a potent bioactive compound with numerous physiological and psychological functions. In this study, we investigated whether B. adolesentis could be used for mass production of GABA.

Results

The B. adolescentis 4–2 strain isolated from a healthy adult human produced approximately 14 mM GABA. It carried gadB and gadC, which encode glutamate decarboxylase and glutamate GABA antiporter, respectively. We constructed pKKT427::Pori-gadBC and pKKT427::Pgap-gadBC plasmids carrying gadBC driven by the original gadB (ori) and gap promoters, respectively. Recombinants of Bifidobacterium were then constructed. Two recombinants with high production abilities, monitored by two different promoters, were investigated. GABA production was improved by adjusting the fermentation parameters, including the substrate concentration, initial culture pH, and co-factor supplementation, using response surface methodology. The optimum initial cultivation pH varied when the promoter region was changed. The ori promoter was induced under acidic conditions (pH 5.2:4.4), whereas the constitutive gap promoter showed enhanced GABA production at pH 6.0. Fed-batch fermentation was used to validate the optimum fermentation parameters, in which approximately 415 mM GABA was produced. The conversion ratio of glutamate to GABA was 92–100%.

Conclusion

We report high GABA production in recombinant B. adolescentis. This study provides a foundation for using Bifidobacterium as a cell factory platform for industrial production of GABA.

A Method of Direct Quantitation of Lactobacillus spp. in Intestinal Contents Based on Real-Time PCR

The method of direct quantitation of Lactobacillus spp. and L. acidophilus in intestinal contents based on real-time PCR was developed. It does not require culturing and allows estimating the number of living lactobacilli cells (measured in lg CFU) in absolute quantitative PCR format.

A qPCR-based method for rapid quantification of six intestinal homeostasis-relevant bacterial genera in feces

Aim: Developing efficient methods for monitoring the complex microbial community to rapidly assess the health status. Materials & methods: The qPCR-based method was developed, verified and in situ applied in fecal samples. Results: Six primer pairs with high specificity were designed to perform qPCR assays under a unified reaction condition within 2.5 h. The limits of detection, amplification efficiency and feasibility of the qPCR-based method established here were verified. In situ application of 18 fecal samples showed that the amounts of Bacteroides, Streptococcus and Bifidobacterium in colorectal cancer patient feces were obviously lower than those of healthy volunteers. Conclusion: This qPCR-based method was a reliable tool for rapid quantification of the six intestinal homeostasis relevant bacterial genera in feces.

Bacterial Diversity of Breast Milk in Healthy Spanish Women: Evolution from Birth to Five Years Postpartum

The objective of this work was to characterize the microbiota of breast milk in healthy Spanish mothers and to investigate the effects of lactation time on its diversity. A total of ninety-nine human milk samples were collected from healthy Spanish women and were assessed by means of next-generation sequencing of 16S rRNA amplicons and by qPCR. Firmicutes was the most abundant phylum, followed by Bacteroidetes, Actinobacteria, and Proteobacteria. Accordingly, Streptococcus was the most abundant genus. Lactation time showed a strong influence in milk microbiota, positively correlating with Actinobacteria and Bacteroidetes, while Firmicutes was relatively constant over lactation. 16S rRNA amplicon sequencing showed that the highest alpha-diversity was found in samples of prolonged lactation, along with wider differences between individuals. As for milk nutrients, calcium, magnesium, and selenium levels were potentially associated with Streptococcus and Staphylococcus abundance. Additionally, Proteobacteria was positively correlated with docosahexaenoic acid (DHA) levels in breast milk, and Staphylococcus with conjugated linoleic acid. Conversely, Streptococcus and trans-palmitoleic acid showed a negative association. Other factors such as maternal body mass index or diet also showed an influence on the structure of these microbial communities. Overall, human milk in Spanish mothers appeared to be a complex niche shaped by host factors and by its own nutrients, increasing in diversity over time.

Effect of the standard herbal preparation, STW5, treatment on dysbiosis induced by dextran sodium sulfate in experimental colitis

BACKGROUND

The standardized herbal preparation, STW 5, is effective clinically in functional gastrointestinal disorders and experimentally in ulcerative colitis (UC). The present study explores whether the beneficial effect of STW 5 involves influencing the intestinal microbiota.

METHODS

UC was induced in Wistar rats by feeding them 5% dextran sodium sulfate (DSS) in drinking water for 7 days. Rats were treated concurrently with STW 5 and sacrificed 24 h after last drug administration. Fecal samples were used to determine changes in the abundance of selected microbial phyla and genera using real-time PCR.

RESULTS

Induction of UC led to dysbiosis and changes in the gut microbiota. The changes included an increase in some genera of the Firmicutes, namely Enterococcus, and a decrease in others, namely Blautia, Clostridium, and Lactobacillus. DSS further induced a marked increase in the abundance of Bacteroidetes and Proteobacteria as well as in the relative abundance of Actinobacteria and its genus Bifidobacterium. Methanobrevibacter levels (phylum Euryarchaeota) were also increased. Microbial dysbiosis was associated with changes in various parameters of colonic inflammation. STW 5 effectively guarded against those changes and significantly affected the indices of edema and inflammation in the UC model. Changes in colon length, colon mass index, inflammatory and apoptotic markers, and histological changes induced by DSS were also prevented.

CONCLUSIONS

Dysbiosis plays a contributing role in the development of DSS-induced UC. Derangements in the microbial flora and associated inflammatory processes were largely prevented by STW 5, suggesting that this effect might contribute towards its beneficial usefulness in this condition.

Microbial community structure and composition is associated with host species and sex in Sigmodon cotton rats

BACKGROUND

The cotton rat (genus Sigmodon) is an essential small animal model for the study of human infectious disease and viral therapeutic development. However, the impact of the host microbiome on infection outcomes has not been explored in this model, partly due to the lack of a comprehensive characterization of microbial communities across different cotton rat species. Understanding the dynamics of their microbiome could significantly help to better understand its role when modeling viral infections in this animal model.

RESULTS

We examined the bacterial communities of the gut and three external sites (skin, ear, and nose) of two inbred species of cotton rats commonly used in research (S. hispidus and S. fulviventer) by using 16S rRNA gene sequencing, constituting the first comprehensive characterization of the cotton rat microbiome. We showed that S. fulviventer maintained higher alpha diversity and richness than S. hispidus at external sites (skin, ear, nose), but there were no differentially abundant genera. However, S. fulviventer and S. hispidus had distinct fecal microbiomes composed of several significantly differentially abundant genera. Whole metagenomic shotgun sequencing of fecal samples identified species-level differences between S. hispidus and S. fulviventer, as well as different metabolic pathway functions as a result of differential host microbiome contributions. Furthermore, the microbiome composition of the external sites showed significant sex-based differences while fecal communities were not largely different.

CONCLUSIONS

Our study shows that host genetic background potentially exerts homeostatic pressures, resulting in distinct microbiomes for two different inbred cotton rat species. Because of the numerous studies that have uncovered strong relationships between host microbiome, viral infection outcomes, and immune responses, our findings represent a strong contribution for understanding the impact of different microbial communities on viral pathogenesis. Furthermore, we provide novel cotton rat microbiome data as a springboard to uncover the full therapeutic potential of the microbiome against viral infections.

Galacto-oligosaccharides supplementation in prefrail older and healthy adults increased faecal bifidobacteria, but did not impact immune function and oxidative stress

BACKGROUND & AIMS

Ageing is associated with an increased risk of frailty, intestinal microbiota perturbations, immunosenescence and oxidative stress. Prebiotics such as galacto-oligosaccharides (GOS) may ameliorate these ageing-related alterations. We aimed to compare the faecal microbiota composition, metabolite production, immune and oxidative stress markers in prefrail elderly and younger adults, and investigate the effects of GOS supplementation in both groups.

METHODS

In a randomised controlled cross-over study, 20 prefrail elderly and 24 healthy adults received 21.6 g/day Biotis™ GOS (containing 15.0 g/day GOS) or placebo. Faecal 16S rRNA gene-based microbiota and short-chain fatty acids were analysed at 0, 1 and 4 weeks of intervention.Volatile organic compounds were analysed in breath, and stimulated cytokine production, CRP, malondialdehyde, trolox equivalent antioxidant capacity (TEAC) and uric acid (UA) in blood at 0 and 4 weeks.

RESULTS

Principle coordinate analysis showed differences in microbial composition between elderly and adults (P≤0.05), with elderly having lower bifidobacteria (P≤0.033) at baseline. In both groups, GOS affected microbiota composition (P≤0.05), accompanied by increases in bifidobacteria (P<0.001) and decreased microbial diversity (P≤0.023). Faecal and breath metabolites, immune and oxidative stress markers neither differed between groups (P ≥ 0.125) nor were affected by GOS (P ≥ 0.236). TEAC values corrected for UA were higher in elderly versus adults (P<0.001), but not different between interventions (P ≥ 0.455).

CONCLUSIONS

Elderly showed lower faecal bifidobacterial (relative) abundance than adults, which increased after GOS intake in both groups. Faecal and breath metabolites, parameters of immune function and oxidative stress were not different at baseline, and not impacted by GOS supplementation. CLINICALTRIALS.

GOV WITH STUDY ID NUMBER

NCT03077529.

Cross-feeding between Bifidobacterium infantis and Anaerostipes caccae on lactose and human milk oligosaccharides

The establishment of the gut microbiota immediately after birth is a dynamic process that may impact lifelong health. At this important developmental stage in early life, human milk oligosaccharides (HMOs) serve as specific substrates to shape the gut microbiota of the nursling. The well-orchestrated transition is important as an aberrant microbial composition and bacterial-derived metabolites are associated with colicky symptoms and atopic diseases in infants. Here, we study the trophic interactions between an HMO-degrader, Bifidobacterium infantis and the butyrogenic Anaerostipes caccae using carbohydrate substrates that are relevant in the early life period including lactose and total human milk carbohydrates. Mono- and co-cultures of these bacterial species were grown at pH 6.5 in anaerobic bioreactors supplemented with lactose or total human milk carbohydrates. A. caccae was not able to grow on these substrates except when grown in co-culture with B. infantis, leading to growth and concomitant butyrate production. Two levels of cross-feeding were observed, in which A. caccae utilised the liberated monosaccharides as well as lactate and acetate produced by B. infantis. This microbial cross-feeding points towards the key ecological role of bifidobacteria in providing substrates for other important species that will colonise the infant gut. The progressive shift of the gut microbiota composition that contributes to the gradual production of butyrate could be important for host-microbial crosstalk and gut maturation.

Effect of Alliaceae Extract Supplementation on Performance and Intestinal Microbiota of Growing-Finishing Pig

Simple Summary

The increasing interest in phytogenics for use with livestock, especially swine and poultry, is mainly due to their antimicrobial, antioxidant, growth-promoting, and gut microbiome modulation properties, which makes them ideal candidates to mitigate the negative effects of the ban on antibiotic growth promoters in the European Union. We tested the ability of Allium spp. extract (containing garlic and onion), one of the best-known phytogenics, used in pig feed, to improve growth performance through modulation of the microbiome and changes in the metabolism of short-chain fatty acids in the gut tract. The promising results obtained in the present study suggested that Allium spp. extracts had the potential to be used in feeding pigs to improve growth performances by modulating the microbiota and metabolism of short-chain fatty acids.

Abstract

The aim of the present study was to ascertain whether an Allium spp. extract rich in organosulfur compounds, such as propyl thiosulfonate (PTSO), added to the feed of growing-finishing pigs at 5 g/kg enhances growth performance or affects the fecal microbiome, the levels of short-chain fatty acids, or the antioxidant capacity of the animals. Fifty male growing pigs (large white) of 23.07 ± 2.87 kg average body weight were randomly allotted to two treatments in a 103-day trial. The trial was divided into two periods, an initial growing phase (56-days) and a finishing phase (47-days). Two dietary treatments for each phase (growing and finishing) were used: a control diet (CON) and an experimental diet consisting of the control diet to which 5 g/kg of Allium spp. extract was added to substitute sepiolite (GAR). Throughout the study, body weight, average daily gain (kg/day, ADG), feed intake (kg/day), and feed conversion ratio (kg/kg) were measured, while the backfat thickness and muscle depth were determined at the end of the study. Besides, feces samples were taken for bacterial counts by means of real-time PCR and short-chain fatty acid (SCFA) profile determination, and the antioxidant capacity was assessed in serum and saliva. In the animals receiving Allium spp. extract (5 g/kg) in the feed, ADG increased (p < 0.05) throughout the trial, Salmonella spp. and Clostridium spp. counts in feces had decreased (p < 0.05) when measured on day 56, and, by day 103, Salmonella spp., Clostridium spp., and Enterobacteriaceae counts had decreased (p < 0.05) and Lactobacillus spp. counts had increased (p < 0.01) in feces. Regarding the SCFA profile in feces and antioxidant capacity measured in serum and saliva, supplementation with Allium spp. extract significantly increased the levels of propionic, isobutyric, and isovaleric acids and the percentage of total branched fatty acids, while the c2/c3 and (c2 + c4)/c3 ratios were lower (p < 0.05) in feces; the Trolox equivalent antioxidant capacity and the cupric reducing antioxidant capacity levels in serum were significantly higher in the same pigs on day 103 than on day 0. Consequently, based on the current results, Allium spp. extract rich in organosulfur compounds, added to the diet at 5 g/kg, had a beneficial effect on the microbiota and would seem to be a possible alternative for increasing the growth performance of growing-finishing pigs. However, further studies on the effects of Allium spp. supplementation on carcass quality are necessary.

Early supplementation of Saccharomyces cerevisiae boulardii CNCM I-1079 in newborn dairy calves increases IgA production in the intestine at 1 week of age

The early development of immunity and microbiota in the gut of newborn calves can have life-long consequences. Gut microbiota and the intestinal barrier interplay after birth, establishing a homeostatic state whereby mucosal cells cohabit with microorganisms to develop a healthy gut. We hypothesized that postnatal codevelopment of gut immunity and microbiota could be influenced by early-life supplementation with live yeast. Starting from birth, calves either received a daily supplementation of Saccharomyces cerevisiae boulardii CNCM I-1079 (SCB, 10 × 10⁹ cfu/d, n = 10) in the morning meal for 7 d or no supplementation (n = 10). Each animal received 2 adequate colostrum replacer meals at 2 and 12 h of life (expected total IgG fed = 300 g) before being fed milk replacer twice a day. Passive transfer of immunity (total protein, IgG, and IgA) through colostrum was evaluated and endogenous production of IgA was investigated by measuring IgA-producing plasma cells, IgA relative gene expression (PIGR and CD79A), and secretory IgA concentration in the gut. The concentration of targeted microbial groups was evaluated with quantitative PCR in the gut digesta collected at d 7 of life. Early SCB supplementation did not impair immunoglobulin absorption and all calves had successful passive transfer of immunity (serum IgG concentration >15 mg/mL at d 1 and d 7 of age). Although the expression of IgA relative gene expression (PIGR and CD79A) was not different, SCB calves had higher secretory IgA concentrations in the ileum (1.98 ± 0.12 mg/g of dry matter; DM) and colon (1.45 ± 0.12 mg/g of DM) digesta compared with control animals (1.18 and 0.59 ± 0.12 mg/g of DM, respectively). In addition, the number of IgA-producing plasma cells were greater in both ileum (2.55 ± 0.40 cells/mm²) and colon (3.03 ± 0.40 cells/mm²) tissues for SCB calves compared with control (respectively 1.00 ± 0.40 and 0.60 ± 0.42 cells/mm²). Endogenous IgA production in the gut of SCB calves was enhanced, which could make them less prone to pathogen intrusion. In addition, SCB calves had higher Lactobacillus and tended to have higher Faecalibacterium prausnitzii in the jejunum compared with control calves, which suggests that SCB supplementation during early-life gut colonization may have a positive effect in newborn calves. Direct SCB supplementation or the cross-talk between SCB and bacteria may be responsible for stimulating IgA production and may play a key role in shaping early colonization in the gut of newborn calves.

Effect of colostrum feeding strategies on the expression of neuroendocrine genes and active gut mucosa-attached bacterial populations in neonatal calves

Colostrum feeding is vital for the development of the immune system and gastrointestinal tract in neonatal calves; however, it is currently unknown whether different colostrum feeding strategies affect their neuroendocrine system and potentially the gut-brain axis. The present study investigated the effect of 3 different colostrum feeding regimens on the expression of neuroendocrine genes in adrenal glands and gastrointestinal tissues and on the abundance of intestinal commensal bacteria. Holstein bull calves were fed colostrum immediately after birth and randomly assigned to 3 groups: whole milk (n = 8), mixture of 50% colostrum and 50% whole milk (n = 8), and colostrum (CF; n = 8) for 72 h with 12-h intervals. Adrenal glands, ileum, and colon tissues were collected at 75 h and were subjected to the expression of 11 targeted neuroendocrine genes and the abundance of tissue mucosa-associated bacteria measurement using quantitative real-time PCR and quantitative PCR, respectively. The expressions of all targeted genes were detected, and the expression of α-adrenergic receptor (ADRA1A) gene was affected by CF in adrenal glands and gut tissues. In addition, CF upregulated the expression of HTR4 (serotonin receptor) and SLC4A4 (serotonin transporter) genes in the ileum and increased the abundance of active Lactobacillus spp. and Escherichia coli (as detected at RNA level) associated with ileum and colon tissue. Furthermore, there were positive correlations between the abundance of active Lactobacillus spp. and E. coli with expression of HTR2B and HTR4 genes in the colon, suggesting that extended colostrum feeding strategies may affect the interaction between gut microbiota and host endocrine functions in neonatal calves.

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

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

Investigating the gut-brain axis in a neurodevelopmental rodent model of schizophrenia

Background

Although the aetiology of schizophrenia remains unknown, it has been suggested that it might occur in response to alterations in the gut-brain axis (GBA), the bi-directional communication system between the gut and the brain. The current study aimed to determine whether the “two-hit” animal model of neuropsychopathology (maternal immune activation combined with adolescent cannabinoid exposure), produced abnormalities in the GBA

Method

Pregnant Wistar rats were administered the viral mimetic polyI:C on gestational day 19 and offspring were administered the synthetic cannabinoid HU210 from postnatal days 35–48. Evidence of GBA activation was assessed in the hypothalamus, colon and fecal samples from male and female offspring at adolescence and adulthood

Results

Findings were sex-specific with adolescent female offspring exhibiting an increased hypothalamic inflammatory profile, increased hypothalamic CRHR1 mRNA, and decreased fecal expression of Bifidobacterium longum, however, no changes were detected in colonic inflammation or integrity.

Conclusion

These results indicate that the rat two-hit model, documented to produce behavioural and neuroanatomical abnormalities, also produces hypothalamic and microbiota abnormalities. The results also demonstrate significant sex differences, suggesting that this model may be useful for investigating the role of the GBA in the aetiology of neurodevelopmental disorders such as schizophrenia.

•

Combined MIA and ACE induces sex-specific alterations in hypothalamic inflammation.

•

Combined MIA and ACE increases hypothalamic CRHR1 expression.

•

Combined MIA and ACE decreases fecal expression of Bifidobacterium longum.

The effect of storage conditions on microbial communities in stool

Microbiome research has experienced a surge of interest in recent years due to the advances and reduced cost of next-generation sequencing technology. The production of high quality and comparable data is dependent on proper sample collection and storage and should be standardized as far as possible. However, this becomes challenging when samples are collected in the field, especially in resource-limited settings. We investigated the impact of different stool storage methods common to the TB-CHAMP clinical trial on the microbial communities in stool. Ten stool samples were subjected to DNA extraction after 48-hour storage at -80°C, room temperature and in a cooler-box, as well as immediate DNA extraction. Three stool DNA extraction kits were evaluated based on DNA yield and quality. Quantitative PCR was performed to determine the relative abundance of the two major gut phyla Bacteroidetes and Firmicutes, and other representative microbial groups. The bacterial populations in the frozen group closely resembled the immediate extraction group, supporting previous findings that storage at -80°C is equivalent to the gold standard of immediate DNA extraction. More variation was seen in the room temperature and cooler-box groups, which may be due to the growth temperature preferences of certain bacterial populations. However, for most bacterial populations, no significant differences were found between the storage groups. As seen in other microbiome studies, the variation between participant samples was greater than that related to differences in storage. We determined that the risk of introducing bias to microbial community profiling through differences in storage will likely be minimal in our setting.

Method comparison for the direct enumeration of bacterial species using a chemostat model of the human colon

BACKGROUND

Clostridioides difficile infection (CDI) has a high recurrent infection rate. Faecal microbiota transplantation (FMT) has been used successfully to treat recurrent CDI, but much remains unknown about the human gut microbiota response to replacement therapies. In this study, antibiotic-mediated dysbiosis of gut microbiota and bacterial growth dynamics were investigated by two quantitative methods: real-time quantitative PCR (qPCR) and direct culture enumeration, in triple-stage chemostat models of the human colon. Three in vitro models were exposed to clindamycin to induce simulated CDI. All models were treated with vancomycin, and two received an FMT. Populations of total bacteria, Bacteroides spp., Lactobacillus spp., Enterococcus spp., Bifidobacterium spp., C. difficile, and Enterobacteriaceae were monitored using both methods. Total clostridia were monitored by selective culture. Using qPCR analysis, we additionally monitored populations of Prevotella spp., Clostridium coccoides group, and Clostridium leptum group.

RESULTS

Both methods showed an exacerbation of disruption of the colonic microbiota following vancomycin (and earlier clindamycin) exposure, and a quicker recovery (within 4 days) of the bacterial populations in the models that received the FMT. C. difficile proliferation, consistent with CDI, was also observed by both qPCR and culture. Pearson correlation coefficient showed an association between results varying from 98% for Bacteroides spp., to 62% for Enterobacteriaceae.

CONCLUSIONS

Generally, a good correlation was observed between qPCR and bacterial culture. Overall, the molecular assays offer results in real-time, important for treatment efficacy, and allow the monitoring of additional microbiota groups. However, individual quantification of some genera (e.g. clostridia) might not be possible without selective culture.

L-Arabinose Elicits Gut-Derived Hydrogen Production and Ameliorates Metabolic Syndrome in C57BL/6J Mice on High-Fat-Diet

Obesity and metabolic syndrome (MS) associated with excess calorie intake has become a great public health concern worldwide. L-arabinose, a naturally occurring plant pentose, has a promising future as a novel food ingredient with benefits in MS; yet the mechanisms remain to be further elucidated. Gut microbiota is recently recognized to play key roles in MS. Molecular hydrogen, an emerging medical gas with reported benefits in MS, can be produced and utilized by gut microbes. Here we show oral L-arabinose elicited immediate and robust release of hydrogen in mice in a dose-and-time-dependent manner while alleviating high-fat-diet (HFD) induced MS including increased body weight especially fat weight, impaired insulin sensitivity, liver steatosis, dyslipidemia and elevated inflammatory cytokines. Moreover, L-arabinose modulated gene-expressions involved in lipid metabolism and mitochondrial function in key metabolic tissues. Antibiotics treatment abolished L-arabinose-elicited hydrogen production independent of diet type, confirming gut microbes as the source of hydrogen. q-PCR of fecal 16S rDNA revealed modulation of relative abundances of hydrogen-producing and hydrogen-consuming gut microbes as well as probiotics by HFD and L-arabinose. Our data uncovered modulating gut microbiota and hydrogen yield, expression of genes governing lipid metabolism and mitochondrial function in metabolic tissues is underlying L-arabinose's benefits in MS.

Association of intestinal oxalate-degrading bacteria with recurrent calcium kidney stone formation and hyperoxaluria: a case-control study

OBJECTIVES

To investigate potential oxalate-degrading bacteria, including Oxalobacter formigenes, Lactobacillus (Lac) and Bifidobacterium (Bif) genera, and Oxalyl-CoA decarboxylase (oxc) encoding Lac (LX) and Bif (BX) species in participants with recurrent calcium kidney stones, and their correlation with 24-h urine oxalate.

PARTICIPANTS AND METHODS

Stool and 24-h urine samples were collected from 58 patients with urolithiasis (29 cases with and 29 without hyperoxaluria) and 29 healthy controls. Absolute quantitation and relative abundance of the bacteria were measured by real-time PCR. The relationship between the investigated bacteria and 24-h urine oxalate were assessed statistically.

RESULTS

The count per gram of stool and relative abundance of O. formigenes, Lac, Bif, LX and BX and the number of participants carrying O. formigenes, LX and BX bacteria were not significantly different between the groups; however, the relative abundance of O. formigenes in the kidney stone group was lower than in healthy controls (P = 0.035). More healthy controls were O. formigenes-positive compared with participants in the kidney stone group (P = 0.052). The results of the linear regression model, including all study participants, showed that the presence of O. formigenes could decrease 24-h urine oxalate (β = -8.4, P = 0.047). Neither Lac and Bif genera nor LX and BX species were correlated with calcium stones or urine oxalate.

CONCLUSION

These results emphasize the role of O. formigenes in kidney stone formation and its role in hyperoxaluria, which may be independent of kidney stone disease. Moreover, our results suggest that, although some Lac and Bif strains have oxalate-degrading potential, they may not be among the major oxalate-degrading bacteria of the gut microbiome.

Dietary probiotic form modulates broiler gut microbiota indices and expression of gut barrier genes including essential components for gut homeostasis

The probiotic form (PF) type and its dietary administration in combination or not with avilamycin (AV) were investigated for their effects on broiler gut microbiota and expression of genes relevant for gut barrier and gut homeostasis. Depending on PF type (i.e. no addition, viable, inactivated) and AV addition (no/yes), 450 one-day-old Cobb male broilers were allocated in 6 treatments (CON, CON + A, ViP, ViP + A, InP and InP + A) according to a 3 × 2 factorial arrangement with 5 replicates of 15 broilers each for 42 days. Significant interactions (P_PF × AV  ≤ 0.05) between PF and AV administration were shown for the ileal mucosa-associated bacteria, the caecal digesta Lactobacillus spp., the molar ratio of the sum of valeric, hexanoic and heptanoic acids and the gene expressions of ileal and caecal IgA and ileal claudin 1. Avilamycin suppressed ileal digesta Lactobacillus spp. (P_AV  < 0.001) and caecal digesta Clostridium perfringens subgroup (P_AV  = 0.018) and modulated the intestinal fermentation intensity and pattern. The viable PF had the higher levels of ileal digesta Bacteroides spp. (P_PF  = 0.021) and caecal digesta Lactobacillus spp. (P_PF  = 0.038) compared with the other two PF. Probiotic form modulated the microbial metabolic activity in the ileum and caeca with the viable PF being the most noteworthy in terms of effects regarded as beneficial. Furthermore, the viable PF resulted in reduced expression of caecal Toll-like receptors TLR2B (P_PF  = 0.026) and TLR4 (P_PF  = 0.011) and transcription factor NFΚΒ1 (P_PF  = 0.002), which could be considered as essential for limiting inflammation and preserving gut homeostasis. In conclusion, under non-challenge conditions, probiotic function was shown to depend on PF type and to a lesser degree on co-administration with AV. The importance of probiotic viability for the beneficial modulation of important gut components towards a reduced state of physiological inflammation has been highlighted.

Modulation of broiler gut microbiota and gene expression of Toll-like receptors and tight junction proteins by diet type and inclusion of phytogenics

This study evaluated the effect of reduced dietary energy (ME) and crude protein (CP) levels along with inclusion of a phytogenic feed additive (PFA) on gut microbiota composition and gene expression of Toll-like receptor(s) (TLR), tight junction proteins, and inflammatory cytokines expressed in secondary lymphoid organs. Depending on dietary ME and CP level down regulation and the inclusion or not of PFA at 125 mg/kg diet, 450 one-day-old male broilers were allocated in the following 6 treatments for 42 D according to a 3 × 2 factorial design: A: diet formulated optimally to meet broiler nutrient requirements; APh: A+PFA; B: suboptimal in ME and CP levels by 3%; BPh: B+PFA; C: suboptimal in ME and CP levels by 6%; CPh: C+PFA. Diet type and PFA supplementation were shown to affect mostly the mucosa-associated microbiota compared to the luminal ones. Ileal mucosa-associated total bacteria (PD= 0.005), Lactobacillus spp. (PD= 0.003), and Clostridium cluster XIVa (PD= 0.009) were affected by diet type with broilers fed diet B having lower levels compared to broilers fed diets A or C. Moreover, diet type affected cecal mucosa-associated Lactobacillus spp. (PD= 0.002) with broilers fed diet C having lower levels compared to broilers fed diets A or B. Supplementation with PFA resulted in higher levels of cecal mucosa-associated Bacteroides (PP= 0.031), Clostridium cluster IV (PP= 0.007), and Clostridium cluster XIVa (PP= 0.039). Diet type affected TLR2 (PD= 0.046) and claudin 5 (PD= 0.027) in cecal epithelium. Lower TLR2 (PP= 0.021) and higher zonula occludens 2 (PP= 0.031) relative gene expressions were seen in ileal epithelium following PFA supplementation. Moreover, in cecal epithelium, PFA supplementation resulted in lower TLR2 (PP < 0.001) and higher zonula occludens 2 (PP= 0.009), claudin 5 (PP= 0.005) and occludin (PP= 0.039) relative gene expressions. There were no significant diet type and PFA effects on cytokines in secondary lymphoid organs, except for a dietary effect on transforming growth factor beta 4 (PD= 0.023) in cecal tonsils. In conclusion, PFA inclusion beneficially modulated elements of gut microbiota, Toll-like signaling molecules and gut tight junction genes.

Broiler gut microbiota and expressions of gut barrier genes affected by cereal type and phytogenic inclusion

The present study assessed the effects of cereal type and the inclusion level of a phytogenic feed additive (PFA) on broiler ileal and cecal gut microbiota composition, volatile fatty acids (VFA) and gene expression of toll like receptors (TLR), tight junction proteins, mucin 2 (MUC2) and secretory immunoglobulin A (sIgA). Depending on cereal type (i.e. maize or wheat) and PFA inclusion level (i.e. 0, 100 and 150 mg/kg diet), 450 one-day-old male broilers were allocated in 6 treatments according to a 2 × 3 factorial arrangement with 5 replicates of 15 broilers each, for 42 d. Significant interactions (P ≤ 0.05) between cereal type and PFA were shown for cecal digesta Bacteroides and Clostridium cluster XIVa, ileal digesta propionic and branched VFA, ileal sIgA gene expression, as well as cecal digesta branched and other VFA molar ratios. Cereal type affected the cecal microbiota composition. In particular, wheat-fed broilers had higher levels of mucosa-associated Lactobacillus (P _CT = 0.007) and digesta Bifidobacterium (P _CT < 0.001), as well as lower levels of total bacteria (P _CT = 0.004) and Clostridia clusters I, IV and XIVa (P _CT ≤ 0.05), compared with maize-fed ones. In addition, cereal type gave differences in fermentation intensity (P _CT = 0.021) and in certain individual VFA molar ratios. Wheat-fed broilers had higher (P ≤ 0.05) ileal zonula occluden 2 (ZO-2) and lower ileal and cecal TLR2 and sIgA levels, compared with maize-fed broilers. On the other hand, PFA inclusion at 150 mg/kg had a stimulating effect on microbial fermentation at ileum and a retarding effect in ceca with additional variable VFA molar patterns. In addition, PFA inclusion at 100 mg/kg increased the ileal mucosa expression of claudin 5 (CLDN5) (P _PFA = 0.023) and MUC2 (P _PFA = 0.001) genes, and at 150 mg/kg decreased cecal TLR2 (P _PFA = 0.022) gene expression compared with the un-supplemented controls. In conclusion, cereal type and PFA affected in combination and independently broiler gut microbiota composition and metabolic activity as well as the expression of critical gut barrier genes including TLR2. Further exploitation of these properties in cases of stressor challenges is warranted.

The Cheese Matrix Modulates the Immunomodulatory Properties of Propionibacterium freudenreichii CIRM-BIA 129 in Healthy Piglets

Propionibacterium freudenreichii is a beneficial bacterium, used as a cheese starter, which presents versatile probiotic properties. These properties are strain-dependent. We hypothesized they may also be delivery vehicle-dependent. In this study, we thus explored in healthy piglets how the cheese matrix affects the immunomodulatory properties of P. freudenreichii. During 2 weeks, three groups of weaned piglets consumed, respectively, P. freudenreichii as a liquid culture (PF-culture), P. freudenreichii under the form of a cheese (PF-cheese), or a control sterile cheese matrix (Cheese-matrix). The in vivo metabolic activity of P. freudenreichii was assessed by determining short chain fatty acids (SCFA) concentration and bifidobacteria population in feces. Whatever the delivery vehicle, P. freudenreichii was metabolically active in piglets' colon and enhanced both bifidobacteria and SCFA in feces. P. freudenreichii consumption decreased the secretion of TNFα and of IL-10 by peripheral blood mononuclear cells (PBMC). It did not alter IL-10, IFNγ, IL-17, and TNFα secretion in mesenteric lymph node immune cells (MLNC). PF-cheese enhanced significantly Treg phenotype, while PF-culture decreased significantly Th17 phenotype in PBMC and MLNC. Remarkably, only PF-cheese induced an increase of Th2 phenotype in PBMC and MLNC. Ex vivo stimulation of PBMC and MLNC by Lipopolysaccharides and Concanavalin A emphasized the difference in the immunomodulatory responses between PF-culture and PF-cheese group, as well as between PBMC and MLNC. This study shows the importance to consider the delivery vehicle for probiotic administration. It confirms the anti-inflammatory potential of P. freudenreichii. It opens new perspectives for the use propionibacteria-fermented products as preventive agents for inflammatory bowel diseases and intestinal infectious diseases.

Gender Difference and Dietary Supplemental Vitamin B6: Impact on Colon Luminal Environment

Colon diseases can be affected by several factors such as gender difference and dietary supplemental vitamin B₆ (B₆). The nutritional status of B₆ is affected by gender difference, leading us to hypothesize that gender difference affects colon luminal environment, which is dependent on B₆ status. To investigate this hypothesis, we fed male and female rats a diet containing 1 mg, 7 mg, or 35 mg pyridoxine HCl/kg diet for 6 wk. We found significantly higher fecal mucin levels in female rats compared to those in male rats. Supplemental B₆ significantly increased fecal mucins and was particularly profound in the female rats. The abundances of cecal and fecal Akkermansia muciniphila (mucin degrader) were unaffected. The fecal mucin levels were significantly correlated with colonic free threonine and serine and with gene expression of colon MUC16, implying that the combined effect of gender and dietary B₆ on fecal mucins was mediated by the alteration in the levels of such amino acids and MUC16 expression. This study further showed the significant effects of gender difference on colonic free amino acids such as threonine, ornithine, asparagine/aspartate ratio, and glutamine/glutamate ratio, cecal and fecal Lactobacillus spp. levels, and colonic gene expressions of MUC16 and TLR8, the factors relating to colon health and diseases. Therefore, our findings suggest that gender difference and dietary B₆ may have an impact on colon diseases by modulating these parameters.

Reliability of a participant-friendly fecal collection method for microbiome analyses: a step towards large sample size investigation

Background

The effects of gut microbiota on human traits are expected to be small to moderate and adding the complexity of the human diseases, microbiome research demands big sample sizes. Fecal samples for such studies are mostly self-collected by participants at home. This imposes an extra level of complexity as sample collection and storage can be challenging. Effective, low-burden collection and storage methods allowing fecal samples to be transported properly and ensuring optimal quality and quantity of bacterial DNA for upstream analyses are necessary. Moreover, accurate assessment of the microbiome composition also depends on bacterial DNA extraction method. The aim of this study was to evaluate the reliability and efficiency of the OMNIgene•GUT kit as a participant-fecal friendly collection method (storage at room temperature for 24 h (O24h) or 7 days (O7d)) in comparison to the standard collection method (Fresh, storage at 4 °C for less than 24 h) in terms of amount of variability and information content accounting for two common DNA extraction methods.

Results

Fourteen fecal samples were collected from healthy individuals (7 males, 7 females). Collection and storage methods did not differ significantly in terms of DNA concentration and Shannon diversity index. Phylum relative abundance showed significant differences for Bacteroidetes, Actinobacteria and Cyanobacteria. The differences were observed between control (Fresh) and O24h methods, but not between Fresh and O7d. These differences were not seen when performing bacterial DNA quantification based on three bacterial groups: Bacteroides spp., Bifidobacterium spp. and Clostridium cluster IV, which represent three major phyla: Bacteroidetes, Actinobacteria and Firmicutes respectively. The two DNA extraction methods differ in terms of DNA quantity, quality, bacterial diversity and bacterial relative abundance. Furthermore, principal component analysis revealed differences in microbial structure, which are driven by the DNA extraction methods more than the collection/storage methods.

Conclusion

Our results have highlighted the potential of using the OMNIgene•GUT kit for collection and storage at ambient temperature, which is convenient for studies aiming to collect large samples by giving participants the possibility to send samples by post. Importantly, we revealed that the choice of DNA extraction method have an impact on the microbiome profiling.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1249-x) contains supplementary material, which is available to authorized users.

Design of Primers for Evaluation of Lactic Acid Bacteria Populations in Complex Biological Samples

Lactic acid bacteria (LAB) are important for human health. However, the relative abundance of LAB in complex samples, such as fecal samples, is low and their presence and diversity (at the species level) is understudied. Therefore, we designed LAB-specific primer pairs based on 16S rRNA gene consensus sequences from 443 species of LAB from seven genera. The LAB strains selected were genetically similar and known to play a role in human health. Prior to primer design, we obtained consistent sequences for the primer-binding sites by comparing the 16S rRNA gene sequences, manually identifying single-stranded primers and modifying these primers using degenerate bases. We assembled primer pairs with product sizes of >400 bp. Optimal LAB-specific primers were screened using three methods: PCR amplification, agarose gel electrophoresis and single-molecule real-time (SMRT) sequencing analysis. During the SMRT analysis procedure, we focused on sequence reads and diversity at the species level of target LAB in three fecal samples, using the universal bacterium primer 27f/1492r as a reference control. We created a phylogenetic tree to confirm the ability of the best candidate primer pair to differentiate amongst species. The results revealed that LAB-specific primer L5, with a product size of 750 bp, could generate 3222, 2552, and 3405 sequence reads from fecal Samples 1, 2, and 3. This represented 14, 13 and 10% of all target LAB sequence reads, respectively, compared with 2, 0.8, and 0.8% using the 27f/1492r primer. In addition, L5 detected LAB that were in low abundance and could not be detected using the 27f/1492r primer. The phylogenetic tree based on the alignments between the forward and reverse primer of L5 showed that species within the seven target LAB genera could be distinguished from each other, confirming L5 is a powerful tool for inferring phylogenetic relationships amongst LAB species. In conclusion, L5 is a LAB-specific primer that can be used for high-throughput sequencing and identification of taxa to the species level, especially in complex samples with relatively low LAB content. This enables further research on LAB population diversity in complex ecosystem, and on relationships between LAB and their hosts.

Trigonelline inhibits intestinal microbial metabolism of choline and its associated cardiovascular risk

Gut microbiota based metabolism of choline produces trimethylamine (TMA) which is further converted to a pro-atherosclerotic metabolite, trimethylamine-N-oxide (TMAO) by flavin monooxygenase (FMO₃). Trigonelline from the plant Trigonella foenum-graecum has been reported for the treatment of CVD. Aim of the present study was to check the effect of trigonelline on the gut microbiota based conversion of TMA to TMAO. Trigonelline was isolated from hydroalcoholic extract of seeds of Trigonella foenum-graecum. The isolated trigonelline was characterized through TLC and UPLC-MS. Anaerobic microbe responsible for the metabolism of choline to TMA was isolated by culturing the human gut microbiota in choline enriched medium. The isolated bacteria was identified at molecular level based on PCR amplification of 1500bp of 16S rRNA gene sequence. Isolated FMO₃ was used for ex vivo conversion of TMA to TMAO. Further, we investigated the effect of trigonelline in isolated gut microbe based metabolism of choline, lipid profile and TMAO levels in mice with or without suppression of gut microbiota with antibiotics. Liquid-liquid purification and chromatographic analysis confirmed the trigonelline purity (87.26%) and which was also confirmed by mass spectroscopy with m/z 137.4 in positive ionization mode. A total of 30 anaerobic microbes responsible for TMA production were isolated and Citrobacter freundii was the superior among others for the production of TMA. In vitro culture of C. freundii in choline enriched medium supplemented with trigonelline resulted in significantly reduction TMA and followed by TMAO production. In ex vivo, a maximum of 85.3% TMAO production was reduced by trigonelline at concentration of about 300 μg/mL. Serum level of lipids and TMAO were significantly altered in choline fed animals with or without suppression of gut microbiota and this phenomenon was reversed upon the oral administration of trigonelline in a dose-dependent manner. This study demonstrates the effect of trigonelline on gut microbiota responsible for choline metabolism and this can be used as a model for evaluation of herbal drugs and its effect in gut microbiota prompted cardiovascular disorders.

In vitro effects of inulin and soya bean oligosaccharide on skatole production and the intestinal microbiota in broilers

The experiment was conducted to investigate the in vitro effects of inulin and soya bean oligosaccharide (SBO) on the metabolism of L-tryptophan (L-try) to skatole production, and the intestinal microbiota in broilers. Treatments were as follows: caecal microbiota control (Cc), Cc + inulin, Cc + SBO, rectal microbiota control (Rc), Rc + inulin and Rc + SBO. Microbial suspensions were anaerobically incubated at 38°C for 24 hr. The results showed that concentrations of skatole and acetic acid were significantly lower in caecal microbiota fermentation broth (MFB) than those in rectal MFB (p < .05). Addition of inulin or SBO significantly decreased the concentrations of indole and skatole and rate of L-try degradation (p < .05). Inulin groups had lower indole than SBO groups (p < .05). PCR-DGGE analysis revealed that addition of inulin or SBO decreased the microbiota richness (p < .05), but no significant differences in Shannon index (p > .05). Four distinct bands were detected in inulin and SBO groups, which were related to two of Bacteroides, one of Firmicutes and Bifidobacteria. Six bands were detected only in control groups, which represented uncultured Rikenellaceae, Roseburia, Escherichia/Shigella dysenteriae, Bacteroides uniformis (T), Parabacteroides distasonis and Enterobacter aerogenes. Populations of Lactobacilli, Bifidobacteria and total bacteria in inulin groups were higher than those in control groups (p < .05). For SBO groups, only population of total bacteria increased (p < .05). However, there were no significant differences in Escherichia coli population among treatments (p > .05). These results suggest that reduced concentrations of skatole and indole in the presence of inulin and SBO may be caused by decrease in L-try degradation rate, which were caused by change in microbial ecosystem and pH value. Uncultured B. uniformis (T) and E. aerogenes may be responsible for degradation of L-try to skatole.

Effect of DS-2969b, a novel GyrB inhibitor, on rat and monkey intestinal microbiota

DS-2969b, a novel GyrB inhibitor, transiently and reversibly altered the counts of limited intestinal microbiota at around 10 μg/g of faecal levels in rats and monkeys. Considering the high activity of DS-2969b against Clostridium difficile, 10 μg/g of faecal levels would be sufficient for clearing C. difficile from the intestine.