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Noncoding RNAs (ncRNAs) play pivotal roles in various biological processes in plants. However, the role of ncRNAs in tapping panel dryness (TPD) of rubber tree (Hevea brasiliensis Muell. Arg.) is largely unknown. Here, the whole transcriptome analyses of bark tissues from healthy and TPD trees were performed to identify differentially expressed long ncRNAs (DELs), microRNAs/miRNAs (DEMs), genes (DEGs) and their regulatory networks involved in TPD. A total of 263 DELs, 174 DEMs and 1574 DEGs were identified in the bark of TPD tree compared with that of healthy tree. Kyoto Encyclopedia of Genes and Genomes analysis revealed that most of the DEGs and targets of DELs and DEMs were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites and plant hormone signal transduction. Additionally, the majority of DEGs and DELs related to rubber biosynthesis were downregulated in TPD trees. Furthermore, 98 DEGs and 44 DELs were targeted by 54 DEMs, 190 DEGs were identified as putative targets of 56 DELs, and 2 and 44 DELs were predicted as precursors and endogenous target mimics of 2 and 6 DEMs, respectively. Based on these, the DEL–DEM–DEG regulatory network involved in TPD was constructed, and 13 hub DELs, 3 hub DEMs and 2 hub DEGs were identified. The results provide novel insights into the regulatory roles of ncRNAs underlying TPD and lay a foundation for future functional characterization of long ncRNAs, miRNAs and genes involved in TPD in rubber tree.

Background Asthma is increasingly prevalent worldwide, and novel strategies to prevent or treat this disease are needed. Probiotic intervention has recently been reported to be effective for asthma prevention. Here, we explored the effects of Faecalibacterium prausnitzii on the development of allergic airway inflammation in a murine model of house dust mite (HDM)-induced allergic asthma. Results Supplementation with living and dead F. prausnitzii blocked eosinophils, neutrophil, lymphocytes, and macrophages influx and alleviated the pathological changes. Moreover, both living and dead F. prausnitzii administration decreased the levels of IL-4, IL-5, IL-13, and IgG1, elevated the regulatory T cells (Tregs) ratio, improved the microbial dysbiosis, and enhanced SCFAs production. The network correlation analysis revealed that the immune indicators were strongly associated with SCFAs production. Based on the linear discriminant analysis effect size (LEfSe), Turicibacter was found as the core genus related to HDM-induced asthma. Living F. prausnitzii treatment enriched Faecalibaculum, Dubosiella, and Streptococcus, while dead F. prausnitzii treatment increased Muribaculaceae and Parabacteroides. Interestingly, both living and dead F. prausnitzii administration enriched Lachnoclostridium and normalized the pathways involving carbohydrate and lipid metabolisms, which might be related to SCFAs production. Conclusion F. prausnitzii exerts an anti-asthmatic effect partly by gut microbiota modulation and SCFAs production, suggesting its promising potential as a probiotic agent for allergic asthma prevention. This article is protected by copyright. All rights reserved.

Brown algae glycan from Laminaria japonica (LJNP) is a heterogeneous glycan with two apparent molecular weights of 1.1 and 37.3 kDa, and is mainly composed of α β-glucan and a few fucosyl residues. To explore the regulation of gut microbiota and the host, LJNP and 2'-fucosyllactose (2'FL) were compared to investigate their effect on mice via oral administration. Using metagenomic and metabolomic analyses, we found that 2'FL mainly relied on Adlercreutzia equolifaciens and Akkermansia muciniphila to improve gut amino acid and bile acid metabolism, whereas LJNP mainly drove Bacteroides vulgatus and Bacteroides uniformis to regulate gut amino acid metabolism and glycometabolism. Moreover, LJNP showed a weight loss effect and better protection of the intestinal barrier than 2'FL. We further employed LJNP and 2'FL on a germ-free mice model. Interestingly, the body weight management was not microbiome mediated. This study showed that LJNP can ameliorate the intestinal barrier through modulation of the gut microbiota, maintain the blood glucose level, and regulate body weight and the antioxidant function. Although the benefits of LJNP on host health were partly revealed, mechanisms such as the weight loss effect require further study.

Bacteroides, an abundant genus in the intestines of mammals, has been recently considered as the next generation probiotics (NGP) candidate due to its potential role in promoting host health. However, the role of Bacteroides in the development of intestinal dysfunctions such as diarrhea, inflammatory bowel disease, and colorectal cancer should not be overlooked. In the present study, we focused on nine most widely occurred and abundant Bacteroides species and discussed their roles in host immunity, glucose and lipid metabolism and the prevention or induction of diseases. Besides, we also discussed the current methods used in the safety evaluation of Bacteroides species and key opinions about the concerns of these strains for the future use.

It is well known that the gut microbiota plays an extremely important role in modulating host physiological functions such as immunity and metabolic homeostasis. In recent years, accumulated evidence has revealed that the gut microbiota can regulate the functions of the central nervous system (CNS) through the gut–brain axis, which provides a novel insight into the interactions between the gut and brain. This review focuses on the molecular mechanism of the crosstalk between the gut microbiota and the brain via the gut–brain axis, and on the onset and development of neurological disorders triggered by gut microbiota dysbiosis. These topics are followed by a critical analysis of potential intervention strategies targeting gut microbiota dysbiosis, including the use of probiotics, prebiotics, synbiotics, and diets. While research on the microbiota–gut–brain axis is still in its relative infancy, clarifying the molecular mechanism that underlies how the gut microbiota regulates neurological functions not only holds the promise of revealing potentially novel pathogeneses of neurological disorders, but also may lead to the development of potential diagnosis biomarkers and intervention strategies targeting microbiota dysbiosis for neurological disorders.

This study investigated the prophylactic effects of five Lactobacillus casei strains on house dust mite (HDM)-induced asthma in mice. BALB/c mice were orally administered with L. casei strains for one week before HDM treatment. Ketotifen and Lactobacillus rhamnosus GG were used as positive controls. All L. casei strains decreased the number of granulocytes and the levels of Th2 and Th17 inflammatory cytokines in the lungs, L. casei3 significantly decreased the airway inflammation score. Further studies showed that L. casei3, L. casei4, and L. casei5 decreased the chemokine levels, L. casei2, L. casei4, and L. casei5 promoted the secretion of secretory immunoglobulin A (sIgA), L. casei2 upregulated the interleukin (IL)-10 levels, and L. casei1 had no effect on these immune indices. L. casei1 and L. casei4 decreased the serum levels of total IgE and HDM-specific IgG1, respectively. L. casei3 and L. casei5 decreased both HDM-specific IgG1 and total IgE levels. L. casei2 did not affect the levels of these immunoglobulins. The gut microbiota analysis revealed that all five L. casei strains enhanced the richness of the gut microbiota mainly by increasing the abundance of Firmicutes, while there were differences at the genus level.Thus, the prophylactic effects of L. casei on HDM-induced mixed chronic airway inflammatory asthma exerted as they differentially affected the immune responses and gut microbiota composition. L. casei3, which exhibited the highest prophylactic effect, increased the acetate and propionate contents in a strain-dependent manner.

Here, we aim to understand the condition of the gut microbiome of Filipino adults in relation to their diet and metabolic status. Compared to rural Albay (n = 67), the gut microbiome of subjects living in urban Manila (n = 25) was more colonized by the order Clostridiales, which was negatively correlated with host carbohydrate consumption. Principal component analysis using the genus composition of the 92 total subjects indicated four microbiome types: one type driven by Prevotella, which was associated with high rice consumption and mainly consisted of healthy Albay subjects, one Clostridiales-driven group containing a number of type 2 diabetes mellitus (T2D) subjects from both Manila and Albay who showed lower butyrate levels in association with a decrease in Mediterraneibacter faecis, and the other two types showing dysbiosis-like microbiomes with Lactobacillus and Bifidobacterium overgrowth, with a high ratio of T2D and obese subjects. Multivariate logistic regression analysis suggested high dietary energy intake, and two Veillonellaeae genera, Dialister and Megasphaera, as T2D risk factors, while Prevotella and M. faecis as anti-T2D factors. In conclusion, low-carbohydrate diets restructured the Prevotella-driven gut microbiome, which may predispose Filipino people with high energy diet to T2D.

The gut microbiota could affect human health and disease. Although disease-associated microbiota alteration has been extensively investigated in the Chinese population, a nationwide Chinese gut microbiota baseline is still lacking. Here we performed 16 S rRNA gene sequencing on fecal samples from 2678 healthy Chinese individuals, who belonged to eight ethnic groups and resided in 63 counties/cities of 28 provinces. We identified four enterotypes, three of which were enriched for Prevotella, Bacteroides, and Escherichia, respectively, whereas the fourth one had no dominant genus. By assessing the association between the gut microbiota and 20 variables belonging to six categories, geography, demography, diet, urbanization, lifestyle, and sampling month, we revealed that geography explained the largest microbiota variation, and clarified the distinct patterns in the associations with staple food type, ethnicity, and urban/rural residence. Specifically, the gut microbiota of Han Chinese and ethnic minority groups from the same sites was more alike than that of the same ethnic minority groups from different sites. Individuals consuming wheat as staple food were predicted to have more microbial genes involving in glucan 1,3-beta-glucosidase and S-adenosyl-l-methionine biosynthesis than those who consumed rice, based on functional prediction. Besides, an appreciable effect of urbanization on decreased intra-individual diversity, increased inter-individual diversity, and increased proportion of the Bacteroides enterotype was observed. Collectively, our study provided a nationwide gut microbiota baseline of the Chinese population and knowledge on important covariates, which are fundamental to translational microbiota research.

The infant gut microbiota plays a critical role in early life growth and derives mainly from maternal gut and breast milk. This study aimed to analyze the differences in the gut microbiota, namely Bifidobacterium and Lactobacillus communities at species level among breast milk as well as maternal and infant feces at different time points after delivery. Fifty-one mother–infant pairs from Indonesia were recruited, and the breast milk and maternal and infant feces were collected and analyzed by high throughput sequencing (16S rRNA, Bifidobacterium groEL and Lactobacillus groEL genes). PCoA results showed bacterial composition was different among breast milk and maternal and infant feces within the first two years. The abundance of Bifidobacterium and Bacteroides were significantly higher in infant feces compared to their maternal feces from birth to two years of age, and maternal breast milk within six months after birth (p &lt, 0.05), whereas the abundance of Blautia, Prevotella, and Faecalibacterium was higher in maternal feces compared to that in breast milk within six months and infant feces within one year after birth, respectively (p &lt, 0.05). The relative abundances of Bacteroides and Lactobacillus was higher and lower in infant feces compared to that in maternal feces only between one and two years of age, respectively (p &lt, 0.05). For Bifidobacterium community at species level, B. adolescentis, B. ruminantium, B. longum subsp. infantis, B. bifidum, and B. pseudolongum were identified in all samples. However, the profile of Bifidobacterium was different between maternal and infant feces at different ages. The relative abundances of B. adolescentis and B. ruminantium were higher in maternal feces compared to those in infant feces from birth to one year of age (p &lt, 0.05), while the relative abundances of B. longum subsp. infantis and B. bifidum were higher in infant feces compared to those in maternal feces beyond three months, and the relative abundance of B. pseudolongum was only higher in infant feces between three and six months (p &lt, 0.05). For Lactobacillus community, L. paragasseri showed higher relative abundance in infant feces when the infant was younger than one year of age (p &lt, 0.05). This study showed bacterial composition at the genus level and Bifidobacterium and Lactobacillus communities at the species level were stage specific in maternal breast milk as well as and maternal and infant feces.

The prevalence of obesity and its associated diseases is increasing. In the current study, 15 obese subjects took part in a 12-week multiphase dietetic protocol incorporating an improved ketogenic diet (MDP-i-KD) (KYLLKS 201806). We investigated the effects of the MDP-i-KD on the anthropometric parameters and the gut microbiota of obese subjects. Our results showed that the MDP-i-KD led to significant reductions in body mass index in obese subjects. The MDP-i-KD significantly decreased the relative abundance of the Lachnospiraceae_ND3007_group, the Eubacterium_hallii_group, and Pseudomonas and Blautia. In addition, gut microbiota co-occurrence networks in obese subjects were restructured to a more healthy condition after weight loss. These results show that the MDP-i-KD enhanced weight loss, which may be associated with dietary-induced changes in the gut microbiome. Our results emphasise the importance of determining the interaction between the host and microbial cells to comprehensively understand the mechanism by which diet affects host physiology and the microbiota.

Background Campylobacter jejuni is the major micro-bacillary pathogen responsible for human coloenteritis. Lactic acid bacteria (LAB) have been shown to protect against Campylobacter infection. However, LAB with a good ability to inhibit the growth of C. jejuni in vitro are less effective in animals and animal models, and have the disadvantages of high cost, a long cycle, cumbersome operation and insignificant immune response indicators. Caenorhabditis elegans is increasingly used to screen probiotics for their anti-pathogenic properties. However, no research on the use of C. elegans to screen for probiotic candidates antagonistic to C. jejuni has been conducted to date. Results This study established a lifespan model of C. elegans, enabling the preselection of LAB to counter C. jejuni infection. A potential protective mechanism of LAB was identified. Some distinct LAB species offered a high level of protection to C. elegans against C. jejuni. The LAB strains with a high protection rate reduced the load of C. jejuni in C. elegans. The transcription of antibacterial peptide genes, MAPK and Daf-16 signalling pathway-related genes was elevated using the LAB isolates with a high protection rate. The reliability of the lifespan model of C. elegans was verified using mice and chickens infected with C. jejuni. Conclusions The results showed that different LAB had different abilities to protect C. elegans against C. jejuni. C. elegans provides a reliable model for researchers to screen for LAB that are antagonistic to C. jejuni on a large scale.

Short-term changes in dietary intake can induce changes in gut microbiome. While various dietary polyphenols have been shown to modulate gut microflora, the acute influence of polyphenol-rich mixed spices has not been explored in a controlled setting. We investigated the effects of a single serving of mixed spices Indian curry consumption, in two separate doses, on the gut microbiome in 15 healthy, Singaporean Chinese males, with age and BMI of 23.5 ± 2.4 years and 22.9 ± 2.2 kg/m2 respectively. We found that a low-polyphenol, no spices Dose 0 Control (D0C) meal led to an increase in Bacteroides and a decrease in Bifidobacterium. In comparison to D0C, there was significant suppression of Bacteroides (p Bifidobacterium (p

Indonesia is a developing country facing the national problem of the growing obesity and diabetes in its population due to recent drastic dietary and lifestyle changes. To understand the link between the gut microbiome, diet, and health of Indonesian people, fecal microbiomes and metabolomes of 75 Indonesian adults in Yogyakarta City, including obese people (n = 21), type 2 diabetes (T2D) patients (n = 25), and the controls (n = 29) were characterized together with their dietary and medical records. Variations of microbiomes showed a triangular distribution in the principal component analysis, driven by three dominant bacterial genera, namely Bacteroides, Prevotella, and Romboutsia. The Romboutsia-driven microbiome, characterized by low bacterial diversity and high primary bile acids, was associated with fat-driven obesity. The Bacteroides-driven microbiome, which counteracted Prevotella but was associated with Ruminococcaceae concomitantly increased with high-carbohydrate diets, showed positive correlation with T2D indices but negative correlation with body mass index. Notably, Bacteroides fragilis was increased in T2D patients with a decrease in fecal conjugated bile acids, particularly tauroursodeoxycholic acid (TUDCA), a farnesoid X receptor (FXR) antagonist with anti-diabetic activity, while these features disappeared in patients administered metformin. These results indicate that the gut microbiome status of Indonesian adults is differently associated with obesity and T2D under their varied dietary habits.

Biofilm formation has evolved as an adaptive strategy for bacteria to cope with harsh environmental conditions. Currently, little is known about the molecular mechanisms of biofilm formation in bifidobacteria. A time series transcriptome sequencing analysis of both biofilm and planktonic cells of Bifidobacterium longum FGSZY16M3 was performed to identify candidate genes involved in biofilm formation. Protein–protein interaction network analysis of 1296 differentially expressed genes during biofilm formation yielded 15 clusters of highly interconnected nodes, indicating that genes related to the SOS response (dnaK, groS, guaB, ruvA, recA, radA, recN, recF, pstA, and sufD) associated with the early stage of biofilm formation. Genes involved in extracellular polymeric substances were upregulated (epsH, epsK, efp, frr, pheT, rfbA, rfbJ, rfbP, rpmF, secY and yidC) in the stage of biofilm maturation. To further investigate the genes related to biofilm formation, weighted gene co-expression network analysis (WGCNA) was performed with 2032 transcript genes, leading to the identification of nine WGCNA modules and 133 genes associated with response to stress, regulation of gene expression, quorum sensing, and two-component system. These results indicate that biofilm formation in B. longum is a multifactorial process, involving stress response, structural development, and regulatory processes.

The rate of obesity is rapidly increasing and has become a health and economic burden worldwide. As recent studies have revealed that the gut microbiota is closely linked to obesity, researchers have used various approaches to modulate the gut microbiota to treat the condition. Dietary composition and energy intake strongly affect the composition and function of the gut microbiota. Intestinal microbial changes alter the composition of bile acids and fatty acids and regulate bacterial lipopolysaccharide production, all of which influence energy metabolism and immunity. Evidence also suggests that remodeling the gut microbiota through intake of probiotics, prebiotics, fermented foods, and dietary plants, as well as by fecal microbiota transplantation, are feasible methods to remediate obesity.

Background Accumulating evidence points to an association between gut microbial abnormalities and depression disorder. The microbiota-gut-brain axis is an emerging target for treating depression using nutritional strategies, considering the numerous limitations of current pharmacological approaches. Here we studied the effect and probable mechanisms of psychobiotic treatment on depression. Methods Chronically stressed C57BL/6J male mice were administered viable Bifidobacterium breve CCFM1025 for 5 weeks prior to behavioral testing. Brain neurological alterations, serum corticosterone, cytokines levels, fecal microbial composition, and short-chain fatty acid (SCFA) content were measured. In addition, the effect of SCFA on 5-hydroxytryptophan (5-HTP) biosynthesis was investigated in an in vitro model of enterochromaffin cells (RIN14B). Results CCFM1025 treatment significantly reduced depression- and anxiety-like behaviors. The hyperactive hypothalamic-pituitary-adrenal response, as well as inflammation, were also alleviated, possibly via regulating the expression of glucocorticoid receptors (Nr3c1). Moreover, CCFM1025 also down-regulated the pCREB-c-Fos pathway but increased the expression of brain-derived neurotrophic factor (BDNF). Meanwhile, chronic stress-induced gut microbial abnormalities were restored, accompanied by increased SCFA and 5-HTP levels. The intestinal 5-HTP biosynthesis positively correlated with fecal SCFA and Bifidobacterium breve levels. Conclusions In summary, Bifidobacterium breve CCFM1025 showed considerable antidepressant-like and microbiota-regulating effects, which opens avenues for novel therapeutic strategies towards treating depression.

Gastrointestinal (GI) microbiota play an important role in human health and wellbeing and the first wave of gut microbes arrives mostly through vertical transmission from mother to child. This study has undertaken to understand the microbiota profile of healthy Southeast Asian mother-infant pairs. Here, we examined the fecal, vaginal and breast milk microbiota of Indonesian mothers and the fecal microbiota of their children from less than 1 month to 48 months old. To determine the immune status of children and the effect of diet at different ages, we examined the level of cytokines, bile acids in the fecal water and weaning food frequency. The fecal microbiota of the children before weaning contained mainly Bacteroides and Bifidobacterium, which presented at low abundance in the samples of mothers. After weaning, the fecal microbiome of children was mainly of the Prevotella type, with decreasing levels of Bifidobacterium, thus becoming more like the fecal microbiome of the mother. The abundance of infant fecal commensals generally correlated inversely with potential pathogens before weaning. The fecal Bifidobacterium in children correlated inversely with the consumption of complex carbohydrates and fruits after weaning. The specific cytokines related to the proliferation and maturation of immunity were found to increase after weaning. A decreasing level of primary bile acids and an increase of secondary bile acids were observed after weaning. This study highlights the change in the GI microbiota of infants to adult-type microbiota after weaning and identifies diet as a major contributing factor.

There is ample scientific and clinical evidence of the effects of gut microbiota on the brain but no definitive evidence that the brain can affect changes in gut microbiota under the bi-directional gut-brain axis concept. As there is no pharmacotherapeutic intervention for the early stages of cognitive decline, research has focused on cognitive stimulation in reversing or slowing the impairment. Elderly patients diagnosed with mild cognitive impairment underwent a randomized-control trial of mindful awareness practice. Neuropsychological assessments, inflammatory markers, and gut microbiota profiles were tested. Here, we report that their cognitive impairment was improved and associated with changes in gut bacterial profile. A cognition-score-dependent-abundance was observed in Ruminococcus vs Recognition Trials (RT), Digit Span Backward (DSB), Semantic Fluency Span (SFS) and Memory Domain (MD); Coprococcus vs DSB, Color Trails Test 2 (CTT2) and Block Design (BD); Parabacteroides vs DSB and SFS; Fusobacterium vs DSB and CTT2; Enterobacteriaceae vs BD and SFS; Ruminococcaceae vs DSB; Phascolarctobacterium vs MD. The study showed for the first-time, alteration in the cognitive capacity leading to the corresponding changes in microbiota profiles. This strongly suggests that signals from the different segments of brain could dictate directly or indirectly the abundances of specific gut microbes.

As an effective means to improve quality of life and prevent diseases, the demand for probiotics and related products has increased in recent years. However, it is still unclear whether a particular probiotic strain will have similar beneficial effects on healthy adults from different regions. In this study, the probiotic Lactobacillus casei Zhang (LCZ) was consumed by healthy adults from six different Asian regions and the changes in gut microbiota were compared using PacBio single molecule, real-time (SMRT) sequencing technology based on samples collected before, during and after consumption of LCZ. Our results reveal that the effect of LCZ consumption on individuals was closely related to the composition of that individual’s basal gut microbiota. A Gut Microbiota Variability Index (GMVI) was proposed to quantitatively compare the effects of LCZ on human gut microecology. Subjects from Xinjiang and Singapore regions had the highest and lowest GMVI, respectively. In general, consumption of LCZ increased the relative abundance of certain beneficial bacteria such as Lactobacillus, Roseburia, Coprococcus and Eubacterium rectale, while it inhibited growth of certain harmful bacteria such as Blautia and Ralstonia pickettii. In addition, consumption of LCZ was responsible for the conversion of some participants from Prevotella copri/Faecalibacterium prausnitzii (PF) enterotype to Faecalibacterium prausnitzii/Bacteroides dorei (FB) enterotype and consistently increased the abundance of lactic acid bacteria in the gut. It also increased/enhanced phosphate metabolic modules, amino acid transport systems, and isoleucine biosynthesis, but conversely decreased lipopolysaccharide biosynthesis. These changes could have health benefits for healthy adults.

The human digestive system is inhabited by a large population of microorganisms, including bacteria, viruses and fungi: the microbiome. While little is currently known about the viruses and fungi populating the gut, the bacterial composition has been widely studied. Within the healthy adult gut, bacterial species from the Bacteroidetes and Firmicutes phyla dominate. These microbes play an important part in the development and maintenance of the immune system, with roles in epithelial barrier integrity, control of pathogenic species, and modulating the T helper subset balance. Altered composition of the microbiome has been observed in several autoimmune conditions and colorectal cancer, and has been found to contribute to disease progression. This chapter will discuss the development of the gut microbiome, its effect on the gastrointestinal immune system, and the consequences of dysbiosis in specific autoimmune disorders and colorectal cancer.

Gut microbiome plays an essential role in asthma development, and probiotic-based manipulation of the gut microbiome has been proposed to prevent asthma. Although the preventive effect of Lactobacillus supplementation against allergies has been reported, the precise Lactobacillus species beneficial for effective prevention of asthma remain unidentified and the underlying mechanisms remain unclear. Therefore, we aimed to investigate the efficacy of oral administration of six Lactobacillus species and the mechanism underlying asthma prevention via gut microbiome modulation. We investigated the effects of oral administration of L. rhamnosus, L. fermentum, L. casei, L. gasseri, L. salivarius, and L. reuteri (five strains of each species) on asthma and gut microbiome of house dust mite (HDM)-treated murine models of asthma. Of these, L. reuteri administration was the most effective: it alleviated airway inflammation, decreased total IgE and HDM-IgG1, and reduced Th2-associated pro-inflammatory cytokines. Moreover, modulation of specific microbial genera by L. reuteri was more effective in asthma prevention than the modulation of the overall microbiota composition. Lactobacillus and Enterococcus were enriched after L. reuteri supplementation and were closely associated with total IgE and IL-13 production. Furthermore, L. reuteri specifically altered the gut microbial function toward butyrate generation. Thus, L. reuteri may reduce the risk of asthma development by modulating specific gut microbiota to improve the lung immune environment. Our study suggests a novel option for gut microbiome manipulation via L. reuteri supplementation for suppression of asthma and other allergic diseases.

A total of 105 yeast isolates was obtained from 15 sourdough samples collected from different regions in China and subjected to random amplified polymorphic DNA (RAPD) analysis. Six species were identified including Pichia membranifaciens, which has not previously been reported in Chinese sourdoughs. Different species of yeast were used in single-culture fermentation to make Chinese steamed bread (CSB). The volatiles of the CSB were captured by solid-phase microextraction method, separated and identified by gas chromatography-mass spectrometry. In total, 41 volatile compounds were found in all the steamed breads. All CSBs showed a similar volatile profile; however, significant differences in the quantity of some volatile compounds were seen among the CSB fermented by different yeast species. A partial least squares discriminant analysis showed that the CSBs could be separated by their characteristic volatile profiles. The study suggested that the aromatic properties of CSB are determined by the yeast used.

Few studies have focused on the capacity of lactic acid bacteria in utilizing soybean carbohydrates by genetic and phenotypic approaches. In the current study, genetic and phenotypic characteristics of soybean carbohydrate metabolism in Leuconostoc mesenteroides, Lactococcus lactis and Streptococcus thermophilus were investigated. The results indicated that all the 3 species have the potential capacity to utilize sucrose with a sucrose phosphoenolpyruvate-dependent phosphotransferase system (PTS) pathway mainly consisted of scrA, sacA, scrK and scrR. Among the 15 strains, only 1 L. lactis strain possessed both sucrose permease and PTS pathway. On the other hand, only Leu. mesenteroides among the 3 species have the genes related to α-galactosidases for potential capacity to metabolize raffinose-family oligosaccharides (RFO) in soybean. Four Leu. mesenteroides strains, DQHXN_Q03M16, FSDLZ60M2, DSCAB2M6 and DQHXN_Q38M5, possessed the complete α-galactosidases gene clusters of lacS-galA-galK-galT and high α-galactosidases activity, which contributed to the capacity of these strains to utilize RFO. These findings provide an approach to investigate the genetic and the phenotypic characteristics of Leu. mesenteroides, L. lactis and S. thermophilus in soybean carbohydrate metabolism for suitable strain selection in soybean fermentation.

Lactic acid bacteria (LAB) are widely used as probiotics in the food industry owing to their beneficial effects on human health. However, numerous antibiotic resistance genes have been found in LAB strains, especially tetracycline resistance genes. Notably, the potential transferability of these genes poses safety risks. To comprehensively evaluate tetracycline resistance in LAB, we determined the tetracycline susceptibility patterns of 478 LAB strains belonging to four genera and eight species. By comparing phenotypes with genotypes based on genome-wide annotations, five tetracycline resistance genes, tet(M), tet(W/N/W), tet(L), tet(S), and tet(45), were detected in LAB. Multiple LAB strains without tetracycline resistance genes were found to be resistant to tetracycline at the currently recommended cutoff values. Thus, based on the minimum inhibitory concentrations of tetracycline for these LAB strains, the species-specific microbiological cutoff values for Lactobacillus (para)gasseri, Lactobacillus johnsonii, and Lactobacillus crispatus to tetracycline were first developed using the Turnidge, Kronvall, and eyeball methods. The cutoff values for Lactiplantibacillus plantarum were re-established and could be used to better distinguish susceptible strains from strains with acquired resistance. Finally, we verified that these five genes play a role in tetracycline resistance and found that tet(M) and tet(W/N/W) are the most widely distributed tetracycline resistance genes in LAB.

Biofilms are aggregates of microorganisms that adhere to the surface of certain substances and produce extracellular polymers to improve their resistance to stress. However, only some Bifidobacterium strains can form biofilms on abiotic surfaces. The study evaluated the biofilm-forming abilities of six Bifidobacterium strains on grape seed flour (GSF) with a particle size of 80–120 μm. Bifidobacterium animalis, Bifidobacterium bifidum, and Bifidobacterium adolescentis formed weak biofilms, whereas Bifidobacterium pseudo, Bifibacterium breve, and Bifidobacterium longum formed strong biofilms on GSF. B. pseudo cells formed biofilm particles with a diameter of 2 mm, and their cell numbers reached 2.04 × 109 CFU/g at 32 h. There were almost no viable cells in the culture without GSF after 60 h; however, the number of biofilm cells on GSF was still over 106 CFU/g, indicating that biofilms improve cell survival. Field-emission scanning electron microscopy revealed the following stages in the bifidobacterial biofilm formation process: adsorption to GSF, secretion of extracellular substance, biofilm maturation and dispersal, and cell death. Collectively, these results strongly suggest that GSF is beneficial for Bifidobacterial biofilm growth, providing a theoretical basis for the production of highly resistant probiotics in the food industry.

The prevalence of atopic dermatitis (AD) has increased and a therapeutic strategy using probiotic intervention has been reported. The effects of different Bifidobacterium (B. breve, B. bifidum, B. animalis, B. infants, and B. adolescentis) on gut microbial changes were explored in 2,4-dinitrofluorobenzene (DNFB)-induced AD, a T helper type 2-dominant allergic disease. Oral administration of Bifidobacterium suppressed skin thickening and mast cell infiltration, blocked pro-inflammatory cytokines (IL-4, CCL11, IL-13, and CCL22), increased IL-10 and IFN-γ, and modulated the microbiome and ecology in the gut. Based on 16S rRNA results, DNFB treatment resulted in gut microbial dysbiosis, characterized by a decrease in the proportion of Firmicutes and an increase in Bacteroidetes. The core microbiome related to AD were also observed (Dorea, Prevotella, Sutterella, Odoribacter, and Pseudomonas). B. breve and B. bifidum treatments increased the relative abundance of Adlercreutzia, Streptococcus, Lactobacillus, Anaerostipes, and Anaerotruncus. The functional modules involved in fructose and mannose metabolism, propanoate metabolism, and fatty acid biosynthesis were upregulated, and these might be related to immune regulation and short-chain fatty acids (SCFA) production. Taken together, these results suggested that Bifidobacterium treatments affected gut microbial composition and structure, altered gut microbial ecosystem, and these alterations were closely associated with inflammation and SCFA production.

Probiotics administration can improve host health. This study aims to determine the effects of probiotics (Lactobacillus casei Zhang and Lactobacillus plantarum P-8) administration on milk production, milk functional components, milk composition, and fecal microbiota of dairy cows. Variations in the fecal bacteria microbiota between treatments were assessed based on 16S rRNA profiles determined by PacBio single molecule real-time sequencing technology. The probiotics supplementation significantly increased the milk production and the contents of milk immunoglobulin G (IgG), lactoferrin (LTF), lysozyme (LYS) and lactoperoxidase (LP), while the somatic cell counts (SCC) significantly decreased (P 0.05). Although the probiotics supplementation did not change the fecal bacteria richness and diversity, significantly more rumen fermentative bacteria (Bacteroides, Roseburia, Ruminococcus, Clostridium, Coprococcus and Dorea) and beneficial bacteria (Faecalibacterium prausnitzii) were found in the probiotics treatment group. Meanwhile, some opportunistic pathogens e.g. Bacillus cereus, Cronobacter sakazakii and Alkaliphilus oremlandii, were suppressed. Additionally, we found some correlations between the milk production, milk components and fecal bacteria. To sum up, our study demonstrated the beneficial effects of probiotics application in improving the quality and quantity of cow milk production.

Increasing evidence points to the effect of the gut microbiota on central nervous system functions. Supplementation of certain microbial strains has been demonstrated to alleviate depressive behaviors and neurological abnormalities. This study took the approach to screen for an anti-depressive Bifidobacterium longum strain from fourteen candidates and systematically verified its effect in a chronic stress-induced depression mice model. B. longum subsp. infantis strain CCFM687 could significantly enhance the biosynthesis of 5-hydroxytryptamine (5-HTP) in vitro in RIN14B cells through up-regulation of the Tph1 gene expression. Administration of CCFM687 in mice significantly improved the scores in behavioral tests and increased the level of 5-HTP and serotonin (5-HT) in the prefrontal cortex (PFC) of the brain. The brain-derived neurotrophic factor (BDNF) in the PFC was also increased, possibly through the 5-HT1A-CREB-BDNF pathway. In addition, CCFM687 alleviated the hyperactivity of the hypothalamic–pituitary–adrenal (HPA) axis response and accordingly reversed the peripheral inflammation status. Moreover, the stress-induced structural and functional dysbiosis of the gut microbiome was improved by CCFM687, through increased alpha diversity and abundance of butyrate-producing bacteria, in conjunction with inhibition of pathogenic gene expression. In summary, these results indicate that supplementation of B. longum subsp. infantis strain CCFM687 may prevent the onset of depression from chronic stress, and RIN14B could serve as an efficient cell model for rapid screening of anti-depressive probiotics.

Emerging studies have reported gut microbial composition plays a key role in alleviating AD clinical symptoms during the probiotic intervention, but the correlation among clinical symptoms, immune responses and gut microbial alteration needs to be explored. Therefore, the objective was to investigate the correlation during Bifidobacterium adolescentis intervention in DNFB-induced AD mice. The mice were randomly divided into nine groups and fed B. adolescentis for 3 weeks. At the end of the experiment, clinical and immune indicators were assessed. Flow cytometry was performed to explore the effect of B. adolescentis on regulatory T cells in the spleen. V3–V4 region of the 16S ribosomal RNA (rRNA) gene was sequenced to evaluate changes in the gut microbiota. Bifidobacteria adolescentis treatments reduced ear and skin thickness and suppressed eosinophils and mast cells infiltration. Th1- and Th2-type responses were regulated and the Tregs population was promoted in the spleen by B. adolescentis treatments. Bifidobacteria adolescentis increased the relative abundance of Lactobacillus but decrease Dorea and Pediococcus. Propionic and butyric acids were increased but isovaleric acid was decreased by B. adolescentis treatment. Besides, the functional modules, such as fatty acid biosynthesis, antigen processing and presentation were upregulated by B. adolescentis Ad1 treatment compared to the DNFB group. Collectively, these results imply that B. adolescentis with the role of immunomodulation promotes Treg differentiation and suppresses Th2 responses, and increases the proportion of Lactobacillus that is positively correlated to increase in propionic acid production, and thus has the potential for AD amelioration.

Constipation, which seriously affects living quality of people, is a common gastrointestinal disease. The engagement of the intestinal flora in the development of symptoms of constipation has been frequently hypothesized. In this study, constipated mice induced by loperamide were used to investige the alleviation of constipation by Bifidobacteria. Bifidobacteria was sorted out according to their adhesive properties into two groups. One group combined multiple strains of Bifidobacterium with adhesion property (CMB1), the other combined multiple strains of Bifidobacterium without adhesion property (CMB2). It was found that CMB1 can alleviate constipation more efficiently by improving the water, propionate and butyrate content in feces, and overall gastrointestinal transit time. Meanwhile, from the perspective of fecal microbiota, CMB1 alleviated constipation mainly by increasing the relative abundances of genera (Bifidobacterium, Lactobacillus, and Prevotella) associated with rapid bowel movement. From the perspective of cecal microbiota, CMB1 alleviated constipation mainly by increasing the relative abundances of genera Lactobacillus, Bacteroides, unclassified S24-7, Dorea, Ruminococcus, Coprococcus, and Rikenella, and decreasing the relative abundances of genera Oscillospira, Odoribacter and Unclassified F16, which are associated with methane production and colonic transit. Overall, changes of microbiota in caecum by CMB1 reflect the stage of constipation in mice more comprehensively than that in feces.

Recent studies have realized the link between gut microbiota and human health and diseases. The question of diet, environment or gene is the determining factor for dominant microbiota and microbiota profile has not been fully resolved, for these comparative studies have been performed on populations of different ethnicities and in short-term intervention studies. Here, the Southern Chinese populations are compared, specifically the children of Guangzhou City (China), Penang City (west coast Malaysia) and Kelantan City (east coast Malaysia). These Chinese people have similar ancestry thus it would allow us to delineate the effect of diet and ethnicity on gut microbiota composition. For comparison, the Penang and Kelantan Malay children were also included. The results revealed that differences in microbiota genera within an ethnicity in different cities was due to differences in food type. Sharing the similar diet but different ethnicity in a city or different cities and living environment showed similar gut microbiota. The major gut microbiota (more than 1% total Operational Taxonomy Units, OTUs) of the children population are largely determined by diet but not ethnicity, environment, and lifestyle. Elucidating the link between diet and microbiota would facilitate the development of strategies to improve human health at a younger age.

Previous research reported that fermented yak milk had a diverse microbial composition. For this study, raw yak milk, qula, and fermented yak milk samples were collected from the Aba Tibetan autonomous region of China. The genus and species microbial composition of these samples were analyzed by high-throughput sequencing of 16S rRNA and groEL gene amplicons, and the volatile profile of the samples was quantified by gas chromatography-mass spectrometry. The results indicated variation in abundance of microbiota at the genus level among the fermented yak milk samples, with Lactobacillus as the most abundant genus in the majority of samples, ranging from 41.6 to 98.3%. The volatile profile of the samples varied among those collected from different villages. Correlations between bacterial composition and volatile compounds of the samples were also observed. Lactobacillus displayed a significant correlation with volatile compounds such as benzaldehyde, 2,3-pentanedione, ethanol, and ethyl acetate, whereas the samples with relatively high abundance of Streptococcus and Lactococcus displayed relatively low contents of volatile compounds.

The heavy metal cadmium (Cd) is a contaminant widely distributed in the food chain. In the present study, 8-week oral administration of a probiotic strain, Lactobacillus plantarum CCFM8610, markedly decreased blood Cd levels in volunteers. Further animal study showed that three L. plantarum strains administered orally exhibited significantly different effects on the regulation of bile acid (BA) metabolism and Cd excretion in mice. Among the strains, L. plantarum CCFM8610 showed the most significant effects on enhancing hepatic BA synthesis, biliary glutathione output, and fecal BA excretion. Biliary Cd output and fecal Cd excretion were markedly increased after L. plantarum CCFM8610 administration, resulting in a marked reduction in tissue Cd levels. The regulation of BA homeostasis and Cd excretion was due to the suppression of the enterohepatic farnesoid X receptor-fibroblast growth factor 15 (FXR-FGF15) axis by L. plantarum CCFM8610 and could be abolished by treatment with the FXR agonist GW4064. The regulatory effects were also related to the gut microbiota, as antibiotic pretreatment reversed L. plantarum CCFM8610-induced effects in BA and Cd metabolism.

Previous research has identified phosphoenolpyruvate-dependent phosphotransferase system and tagatose-6-phosphate (T6P) pathway of lactose/galactose metabolism in Lacticaseibacillus casei groups, which led to no galactose accumulation in fermented milk produced by Lb. paracasei. However, Lb. paracasei preferred lactose to galactose when grown in a mixture of the two sugars, indicating possibility of carbon catabolite repression of galactose catabolism in the fermented milk. Therefore, galactose accumulation was still observed during co-culturing of Lb. paracasei with Streptococcus thermophilus in fermented milk. We demonstrated that the transcriptional regulator lacR acts as a transcriptional repressor of the T6P pathway genes (lacA, lacC and lacD) and lacT acts as a transcriptional activator for genes (lacE) encoding the lactose-transporting PTS in the mixed lactose/galactose CDM medium, indicating possible dual repressive effects of global or local regulation on the carbon catabolism of galactose in Lb. paracasei.

With increasing globalisation, various diets from around the world are readily available in global cities. This study aimed to verify if multiethnic dietary habits destabilised the gut microbiome in response to frequent changes, leading to readily colonisation of exogenous microbes. This may have health implications. We profiled Singapore young adults of different ethnicities for dietary habits, faecal type, gut microbiome and cytokine levels. Subjects were challenged with Lactobacillus casei, and corresponding changes in microbiome and cytokines were evaluated. Here, we found that the majority of young adults had normal stool types (73% Bristol Scale Types 3 and 4) and faecal microbiome categorised into three clusters, irrespective of race and gender. Cluster 1 was dominated by Bacteroides, Cluster 2 by Prevotella, while Cluster 3 showed a marginal increase in Blautia, Ruminococaceae and Ruminococcus, without a predominant microbiota. These youngsters in the three faecal microbiome clusters preferred Western high sugary beverages, Southeast Asian plant-rich diet and Asian/Western diets in rotation, respectively. Multiethnic dietary habits (Cluster 3) led to a gut microbiome without predominant microbiota yet demonstrated colonisation resistance to Lactobacillus. Although Bacteroides and Prevotella are reported to be health-promoting but also risk factors for some illnesses, Singapore-style dietary rotation habits may alleviate Bacteroides and Prevotella associated ill effects. Different immunological outcome was observed during consumption of the lactobacilli among the three microbiome clusters.

This study evaluates the ability ofLactobacillus rhamnosusGG (LGG) to activate DC and neutrophils and modulate T cell activation and the impact of bacterial dose on these responses. Murine bone marrow derived DC or neutrophils were stimulated with LGG at ratios of 5 : 1, 10 : 1, and 100 : 1 (LGG : cells) and DC maturation (CD40, CD80, CD86, CD83, and MHC class II) and cytokine production (IL-10, TNF-α, and IL-12p70) were examined after 2 h and 18 h coculture and compared to the ability of BCG (the present immunotherapeutic agent for bladder cancer) to stimulate these cells. A 2 h exposure to 100 : 1 (high dose) or an 18 h exposure to 5 : 1 or 10 : 1 (low dose), LGG : cells, induced the highest production of IL-12 and upregulation of CD40, CD80, CD86, and MHC II on DC. In DCs stimulated with LGG activated neutrophils IL-12 production decreased with increasing dose. LGG induced 10-fold greater IL-12 production than BCG. T cell IFNγand IL-2 production was significantly greater when stimulated with DC activated with low dose LGG. In conclusion, DC or DC activated with neutrophils exposed to low dose LGG induced greater Th1 polarization in T cells and this could potentially exert stronger antitumor effects. Thus the dose of LGG used for immunotherapy could determine treatment efficacy.

Glycerol production is modulated in some halo-tolerant organisms in response to extracellular osmotic stress. Glycerol-3-phosphate dehydrogenase (GPDH) is a rate-limiting enzyme of glycerol synthesis in both yeast and the green microalgae Dunaliella. In yeast, a High-Osmolarity-Glycerol (HOG) pathway, which is a mitogen-activated protein kinase (MAPK) cascade, has been suggested to activate the expression of GPDH and thus the accumulation of glycerol under osmotic stress. In Dunaliella tertiolecta, however, the osmo-regulatory mechanisms for glycerol synthesis are not well understood. In this study, the homologues of MAPK and GPDH in D. tertiolecta were cloned using Rapid Amplification of cDNA Ends (RACE) to investigate the molecular basis of the osmo-regulatory mechanisms. The isolated cDNA sequences were named DtMAPK (GenBank: KJ930518) and DtGPDH (GenBank: KJ930370), respectively. It was found that after osmotic shock DtMAPK and DtGPDH expression increased within 0.5 h and 1 h, respectively. In additio...

Di-(2-ethylhexyl) phthalate (DEHP) is widely used as a plasticizer, which can enter the body through a variety of ways and exerted multiple harmful effects, including liver toxicity, reproductive toxicity and even glucose metabolism disorder. Many studies have suggested that changes of gut microbiota are closely related to the occurrence of various diseases, but the effects of DEHP exposure on gut microbiota are still unclear. It was found in this study that the damage to different tissues by DEHP on two strains each from two different species of male rodents before puberty was dose and time of exposure dependent, and also depending on the strain and species of rodent. Sprague-Dawley (SD) rats showed highest sensitivity to DEHP exposure, with most severe organ damage, highest Th1 inflammatory response and most significant body weight gain. Correspondingly, the gut microbiota of SD rats showed most significant changes after DEHP exposure. Only SD rats, but not Wistar rats, BALB/c and C57BL/6J mice showed an increase in Firmicutes/Bacteroidetes ratio and Proteobacteria abundance in the fecal samples, which are known to associate with obesity and diabetes. This is consistent with the increasing body weight gain which was only found in SD rats. In addition, the decrease in the level of butyrate, increase in the abundance of potential pathogens and microbial genes linked to colorectal cancer, Parkinson's disease, and type 2 diabetes in the SD rats were associated with issue and functional damages and Th1 inflammatory response caused by DEHP exposure. We postulate that the differential effects of DEHP on gut microbiota may be an important cause of the differences in the toxicity on different strains and species of rodents to DEHP.

Constipation is a disorder that affects people of all ages. Previous study showed Bifidobacterium spp. altered the faecal concentrations of short-chain fatty acids (SCFAs) while relieving constipation. Therefore, we speculated SCFAs might relieve constipation. We evaluated constipation-related indicators, SCFA levels and the faecal microbiota of constipated mice that were fed acylated starches derived from specific SCFAs for 1 month. It confirmed application of acylated starches resolved the issue of SCFAs absorption in small intestine by measuring the concentration of different SCFA in various tissues. Acetylated starch relieved constipation by increasing acetic acid-producing bacteria that were correlated positively with the small intestinal transit rate and water content of faeces, while butylated starch relieved constipation by increasing butyric acid-producing bacteria that were correlated negatively with the time to the first black stool defecation. These results indicated acetic acid and butyric acid play different roles in relieving constipation.

Trillions of microbes have evolved with and continue to live on human beings. With the rapid advances in tools and technology in recent years, new knowledge and insight in cross-talk between the microbes and their hosts have gained. It is the aim of this work to critically review and summarize recent literature reports on the role of microbiota and mechanisms involved in the progress and development of major human diseases, which include obesity, hypertension, cardiovascular disease, diabetes, cancer, Inflammatory Bowel Disease (IBD), gout, depression and arthritis, as well as infant health and longevity. Keywords: Gut microbiota, Human health, Disease

Loss of traditional diets by food globalization may have adverse impact on the health of human being through the alteration of gut microbial ecosystem. To address this notion, we compared the gut microbiota of urban (n = 17) and rural (n = 28) school-aged children in Thailand in association with their dietary habits. Dietary records indicated that children living in urban Bangkok tended to consume modern high-fat diets, whereas children in rural Buriram tended to consume traditional vegetable-based diets. Sequencing of 16S rRNA genes amplified from stool samples showed that children in Bangkok have less Clostridiales and more Bacteroidales and Selenomonadales compared to children in Buriram and bacterial diversity is significantly less in Bangkok children than in Buriram children. In addition, fecal butyrate and propionate levels decreased in Bangkok children in association with changes in their gut microbial communities. Stool samples of these Thai children were classified into five metabolotypes (MTs) based on their metabolome profiles, each characterized by high concentrations of short and middle chain fatty acids (MT1, n = 17), amino acids (MT2, n = 7), arginine (MT3, n = 6), amino acids, and amines (MT5, n = 8), or an overall low level of metabolites (MT4, n = 4). MT1 and MT4 mainly consisted of samples from Buriram, and MT2 and MT3 mainly consisted of samples from Bangkok, whereas MT5 contained three samples from Bangkok and five from Buriram samples. According to the profiles of microbiota and diets, MT1 and MT2 are characteristic of children in Buriram and Bangkok, respectively. Predicted metagenomics indicated the underrepresentation in MT2 of eight genes involved in pathways of butyrate biosynthesis, notably including paths from glutamate as well as pyruvate. Taken together, this study shows the benefit of high-vegetable Thai traditional diets on gut microbiota and suggests that high-fat and less-vegetable urban dietary habits alter gut microbial communities in Thai children, which resulted in the reduction of colonic short chain fatty acid fermentation.

Dajiang-meju have been used as major ingredients for the preparation of traditional spontaneously fermented soybean paste in Northeast China. In this work, we sequenced and analyzed the metagenome of 12 dajiang-meju samples. To complement the metagenome analysis, we analyzed the taxonomic and functional diversity of the microbiota by metaproteomics (LC-MS/MS). The analysis of metagenomic data revealed that the communities were primarily dominated by Enterobacter, Enterococcus, Leuconostoc, Lactobacillus, Citrobacter and Leclercia. Moreover, changes in the functional levels were monitored, and metaproteomic analysis revealed that most of the proteins were mainly expressed by members of Rhizopus, Penicillium and Geotrichum. The number of sequences allocated to fungi in the fermentation process decreased, whereas the number of sequences assigned to bacteria increased with time of fermentation. In addition, functional metagenomic profiling indicated that a series of sequences related to carbohydrates and amino acids metabolism were enriched. Additionally, enzymes associated with glycolysis metabolic pathways were presumed to contribute to the generation of flavor in dajiang-meju. Proteins from different dajiang-meju samples involved in global and overview maps, carbohydrate metabolism, nucleic acid metabolism and energy metabolism were differentially expressed. This information improves the understanding of microbial metabolic patterns with respect to the metaproteomes of dajiang-meju and provides a powerful tool for studying the fermentation process of soybean products.

Pigs are one of the most important economic livestock. Gut microbiota is not only critical to the health but also the production efficiency of pigs. Manipulating gut microbiota relies on the full view of gut microbiome and the understanding of drive forces shaping microbial communities. 16s rDNA sequencing was used to profile microbiota along the longitudinal and radical axes to obtain the topographical map of microbiome in different intestinal compartments in young pigs. Alpha and beta-diversities revealed distinct differences in microbial compositions between the distal ileum and cecum and colon, as well as between the lumen and mucosa. Firmicutes and Proteobacteria dominated in the ileum, constituting 95 and 80% of the luminal and mucosa-attached microbiome. Transitioning from the small intestine to the large intestine, luminal Bacteroidetes increased from 1.69 to 45.98% in the cecum and 40.09% in the colon, while mucosal Bacteroidetes raised from 9 to 35.36% and 27.96%. Concurrently, luminal Firmicutes and Proteobacteria and mucosal-attached Proteobacteria remarkably decreased. By co-occurrence network analyses, Prevotellaceae, Ruminococcaceae, Lachnospiraceae and Veillonellaceae were recognized as the central nodes of luminal microbial network, and Prevotellaceae and Enterobacteriaceae, Caulobacteraceae, Enterococcaceae, Xanthomonadaceae, Pseudomonadaceae were identified as mucosal central nodes. Co-abundance was uncovered among Prevotellaceae, Lachnospiraceae, and Veillonellaceae in the luminal and mucosal microbiome, while opportunistic pathogens from γ-Proteobacteria in the mucosa. Strong co-exclusion was shown between Enterobacteriaceae with Prevotellaceae-centered microbial groups in the lumen. Redundancy analysis found bile acids and short chain fatty acids explained 37.1 and 41% of variations in the luminal microbial composition, respectively. Primary bile acid, taurine- and glycine- conjugated bile acids were positively correlated with Lactobacillaceae, Enterobacteriaceae, Clostridiaceae_1, Peptostreptococcaceae, whereas secondary bile acids, acetate, propionate, butyrate, and valerate were positively correlated with Prevotellaceae, Acidaminococcaceae, Ruminococcaceae, Lachnospiraceae, Desulfovibronaceae, Veillonellaceae. Functional analyses demonstrated that Prevotella, Veillonellaceae, Lachnospiraceae, and Ruminococcaceae were positively correlated with gene functions related to amino acids, energy, cofactors and vitamins metabolism, which are indispensable for the hosts. These results suggested site specific colonization and co-occurrence of swine gut microbiome closely relate to the microenvironment in each niche. Interactions of core gut microbiome greatly contributed to metabolism and/or immunity in the swine intestine.

Bifidobacteria are anaerobes and are difficult to culture in conventional fermentation system. It was observed that Bacillus subtilis natto enhanced growth of Bifidobacterium animalis subsp. lactis v9 by about 3-fold in a whole soybean solid-state co-fermentation, in a non-anaerobic condition. For the purpose of understanding the metabolic interactions between Bif. animalis subsp. lactis v9 and Ba. subtilis natto, the transcriptome of Bif. animalis subsp. lactis v9 and Ba. subtilis natto was analyzed in single and mixed cultures using RNA-Seq. Compared with the single culture, 459 genes of Bif. animalis subsp. lactis v9 were up regulated and 21 were down regulated in the mixed culture with Ba. subtilis natto, with more than 2-fold difference. Predictive metagenomic analyses suggested that Ba. subtilis natto up regulated transport functions, complex carbohydrates and amino acid metabolism, DNA repair, oxydative stress-related functions, and cell growth of Bif. animalis subsp. lactis v9. In the mixed culture with Bif. animalis subsp. lactis v9, only 3 transcripts of Ba. subtilis natto were over-expressed and 3115 were under-expressed with more than 2-fold difference. The highest down-regulated genes were those involved in carbohydrate and amino acid metabolism. The data presented here demonstrated a parasitic-like interaction regulated at the transcription level, between Ba. subtilis natto and Bif. animalis subsp. lactis in the mixed culture. The over-expression of genes involved in substrate uptake and metabolism in Bif. animalis subsp. lactis in the mixed culture nevertheless, led to its higher cell concentration in the nutrient rich whole soybean medium.

To reduce operating costs and membrane fouling of conventional membrane bioreactors (cMBR), a novel MBR using a non-woven fabric membrane (nMBR) was constructed and the performance of the two MBRs was compared for anaerobic ammonium oxidation (anammox) cultivation. The results showed that the start-up period for the nMBR (44 days) was notably shorter than that for the cMBR (56 days), meanwhile the nMBR achieved a 2-times higher nitrogen removal rate (231.5 mg N per L per d) compared to the cMBR (112.3 mg N per L per d). Illumina MiSeq sequencing showed that Candidatus Kuenenia and Candidatus Jettenia were the main distinguished anammox bacteria. FISH analysis revealed that anammox bacteria predominated in both reactors, especially in the nMBR (58%) corresponding to a qPCR analysis of 1.07 × 109 copies per mL (day 120). N2O emission analysis confirmed the advantage of the nMBR in N2O reduction to reduce the influence of greenhouse gas emission while treating identical nitrogen. These results clearly demonstrated that nMBRs could be a prospective choice for anammox start-up and performance enhancement.

The gut microbiota possesses diverse metabolic activities but its contribution towards heterogeneous toxicological responses is poorly understood. Here, we elucidate the role of the liver-gut microbiota axis in underpinning the hepatotoxicity of tacrine. We employed an integrated strategy combining pharmacokinetics, toxicology, metabonomics, genomics and metagenomics to elucidate and validate the mechanism of tacrine-induced hepatotoxicity in Lister hooded rats. Pharmacokinetic studies in rats demonstrated 3.3-fold higher systemic exposure to tacrine in strong responders that experienced transaminitis, revealing enhanced enterohepatic recycling of deglucuronidated tacrine in this subgroup, not attributable to variation in hepatic disposition gene expression. Metabonomic studies implicated variation in gut microbial activities that mapped onto tacrine-induced transaminitis. Metagenomics delineated greater deglucuronidation capabilities in strong responders, based on differential gut microbial composition (e.g. Lactobacillus, Bacteroides and Enterobacteriaceae) and ∼9% higher β-glucuronidase gene abundance compared to non-responders. In the validation study, co-administration with oral β-glucuronidase derived from Escherichia coli and pre-treatment with vancomycin and imipenem significantly modulated the susceptibility to tacrine-induced transaminitis in vivo. Conclusion: Our study establishes the pertinent gut microbial influences in defining the hepatotoxicity of tacrine, providing crucial insights for personalized medicine initiatives. This article is protected by copyright. All rights reserved.

Aims Our objective was to examine the possibility of using SmartRoot, free software based on ImageJ, for the measurement of fine root length, surface area, volume and diameter of Hevea brasiliensis. Methods Photos were taken at heights of 15 and 40 cm from the fine root samples before the samples were sub- jected to comparison for accuracy of measurement of fine root length, surface area, volume and diameter of H. brasiliensis. The same images were analyzed manually and semi-automatically as well. Then the results obtained from SmartRoot were compared with those from WinRhizo, an expensive, popular, professional software for root analysis. Important findings The average normal root mean square errors (NRMSE) between 15 and 40 cm height for fine root length, surface area, volume and diameter were 2.87%, 15.73%, 32.38% and 16.88%, respectively. In addi- tion, the NRMSE between manual and semi-automatic analysis for the same morphological parameters were 3.06%, 21.00%, 40.96% and 11.64%, respectively. Furthermore the NRMSE between SmartRoot and WinRhizo on fine root length, surface area, volume and diameter were 5.31%, 9.37%, 9.61% and 5.77%, respectively, signify- ing a high consistency between the two software systems. The results indicated that it is feasible to employ the SmartRoot system for determination of fine-root morphological parameters of H. brasiliensis due to its satisfac- tory accuracy, reliability, easy operation and time-saving advantages. For better accuracy, photos are recom- mended to be taken at the height of 15 cm and analyzed with the semi-automatic method.

Our objective was to investigate the effects of different delivery and feeding modes on the gut microbiota composition of early infants with special emphasis on Bifidobacterium and Lactobacillus profiles at species level. 16S rRNA V3-V4 regions, bifidobacterial, and lactobacilli groEL genes from infant feces were sequenced by Illumina MiSeq. Gut microbiota abundance was significantly different, where standard vaginally delivered (SVD) and breast-fed (BF) groups were higher in comparison with caesarean section (CS), milk-powder-fed (MPF), and mixed-fed (MF) groups. The genus unclassified Enterobacteriaceae was dominant, followed by Bifidobacterium, which was highly abundant in SVD and BF groups. The dominant Bifidobacterium species in all groups were B. longum subsp. longum, B. longum subsp. infantis and B. animalis subsp. lactis. B. dentium and the diversity of Bifidobacterium in SVD and BF groups were significantly higher. For Lactobacillus profiles, L. rhamnosus and L. gasseri were dominant among all the groups, while Lactobacillus species in CS and MPF groups were more diverse. Functional predictions showed significant differences between delivery mode and feeding groups, such as phosphotransferase system as well as taurine and hypotaurine metabolism. In early infants with different delivery and feeding methods, gut microbiota&mdash, particularly bifidobacteria and lactobacilli communities&mdash, showed significant differences, with strong implications for physiological functions.

Glutaredoxins (GRXs) are a class of small oxidoreductases which modulate various biological processes in plants. Here, we isolated a GRX gene from the rubber tree (Hevea brasiliensis M&uuml, ll. Arg.), named as HbSRGRX1, which encoded 107 amino acid residues with a CPYC active site. Phylogenetic analysis displayed that HbSRGRX1 was more correlated with GRXs from Manihot esculenta Crantz. and Ricinus communis L. HbSRGRX1 was localized in the nuclei of tobacco cells, and its transcripts were preferentially expressed in male flowers and in the high-yield variety Reyan 7-33-97 with strong resistance against cold. The expression levels of HbSRGRX1 significantly decreased in tapping panel dryness (TPD) trees. Furthermore, HbSRGRX1 was regulated by wounding, hydrogen peroxide (H2O2), and multiple hormones. Altogether, these results suggest important roles of HbSRGRX1 in plant development and defense response to TPD and multiple stresses.