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.

Bifidobacteria are key gut commensals that confer various health benefits and are commonly used as probiotics. However, little is known about the population-level variation in gut bifidobacterial composition and its affecting factors. Therefore, we analyzed Bifidobacterium species with amplicon sequencing of the groEL gene on fecal samples of 1674 healthy individuals, who belonged to eight ethnic groups and resided in 60 counties/cities of 28 provinces across China. We found that the composition of the bifidobacterial community was associated with geographical factors, demographic characteristics, staple food type, and urbanization. First, geography, which reflects a mixed effect of other variables, explained the largest variation in the bifidobacterial profile. Second, middle adolescence (age 14-17) and age 30 were two key change points in the bifidobacterial community development, and a bifidobacterial community resembling that of adults occurred in middle adolescence, which is much later than the maturation of the whole gut microbial community at approximately age 3. Third, each ethnicity showed a distinct bifidobacterial profile, and the remarkable amount of unknown Bifidobacterium species in the Tibetan gut suggested undiscovered biodiversity. Fourth, wheat as the main staple food promoted the flourish of B. adolescentis and B. longum. Fifth, alpha diversity of the bifidobacterial community decreased with urbanization. Collectively, our findings provide insight into the environmental and host factors that shape the human gut bifidobacterial community, which is fundamental for precision probiotics.

Cadmium (Cd) is an environmental pollutant that is toxic to almost every human organ. Oral supplementation with lactic acid bacteria (LAB) has been reported to alleviate cadmium toxicity. However, research on the mitigation of cadmium toxicity by LAB is still limited to inorganic cadmium, which is not representative of the varied forms of cadmium ingested daily. In this study, different foodborne forms of cadmium were adopted to establish an in vivo toxicity model, including cadmium-glutathione, cadmium-citrate, and cadmium-metallothionein. The ability of Lactobacillus plantarum CCFM8610 to reduce the toxic effects of these forms of cadmium was further investigated. The 16S rRNA gene sequencing and metabolomics technologies based on liquid chromatography with tandem mass spectrometry (LC-MS/MS) were adopted for the exploration of relevant protective mechanisms. The results demonstrated that the consumption of CCFM8610 can reduce the content of cadmium in mice and relieve the oxidative stress caused by different food-derived forms of cadmium, indicating that CCFM8610 has a promising effect on the remediation of the toxic effects of cadmium food poisoning. Meanwhile, protective effects on gut microflora and serum metabolites might be an important mechanism for probiotics to alleviate cadmium toxicity. This study provides a theoretical basis for the application of L. plantarum CCFM8610 to alleviate human cadmium poisoning.

Campylobacter is a well-known food-borne pathogen that causes human gastroenteritis. Food products that contain Campylobacter may also be contaminated by other pathogens, however, whether this multiple contamination leads to more severe infection remains unclear. In this study, mice were gavaged with Campylobacter jejuni and other food-borne pathogenic bacteria to mimic a multiple infection. It was demonstrated that the C. jejuni load was elevated when the mice were co-infected with C. jejuni and Salmonella typhimurium, and the campylobacteriosis that followed was also enhanced, with features of decreased body weight, heavier bloody stools and more pronounced inflammatory changes to the colon. In addition, infection with C. jejuni was also promoted by co-infection with entero-invasive Escherichia coli but unaffected over time. In contrast to S. typhimurium and entero-invasive E. coli, co-infection by Listeria monocytogenes showed little effect on C. jejuni infection and even hindered its progress. In addition, the intestinal microecology was also affected by co-infection of C. jejuni with other pathogens, with an increased relative abundance of unclassified Enterobacteriaceae, decreased levels of butyric acid and changes in the abundance of several genera of gut microbe, which suggests that some food-borne pathogenic bacteria might affect the progression of C. jejuni infection in mice by influencing the composition of the gut microbiota and the resulting changes in SCFA levels. Collectively, our findings suggest that co-infection of Campylobacter with other pathogenic bacteria can impact on the progression of infection by C. jejuni in mice, which may also have implication for the etiology of Campylobacter on human health.

Amino acids comprise the majority of the flavor compounds in soy sauce. A portion of these amino acids are formed from the biosynthesis and metabolism of the fungus Aspergillus oryzae; however, the metabolic pathways leading to the formation of these amino acids in A. oryzae remain largely unknown. We sequenced the transcriptomes of A. oryzae 100-8 and A. oryzae 3.042 under similar soy sauce fermentation conditions. 2D gel electrophoresis was also used to find some differences in protein expression. We found that many amino acid hydrolases (endopeptidases, aminopeptidases, and X-pro-dipeptidyl aminopeptidase) were expressed at much higher levels (mostly greater than double) in A. oryzae 100-8 than in A. oryzae 3.042. Our results indicated that glutamate dehydrogenase may activate the metabolism of amino acids. We also found that the expression levels of some genes changed simultaneously in the metabolic pathways of tyrosine and leucine and that these conserved genes may modulate the function of the metabolic pathway. Such variation in the metabolic pathways of amino acids is important as it can significantly alter the flavor of fermented soy sauce.

As a long-standing biomedical model, rats have been frequently used in studies exploring the correlations between gastrointestinal (GI) bacterial biota and diseases. In the present study, luminal and mucosal samples taken along the longitudinal axis of the rat digestive tract were subjected to 16S rRNA gene sequencing-based analysis to determine the baseline microbial composition. Results showed that the community diversity increased from the upper to lower GI segments and that the stratification of microbial communities as well as shift of microbial metabolites were driven by biogeographic location. A greater proportion of lactate-producing bacteria (such as Lactobacillus, Turicibacter and Streptococcus) were found in the stomach and small intestine, while anaerobic Lachnospiraceae and Ruminococcaceae, fermenting carbohydrates and plant aromatic compounds, constituted the bulk of the large-intestinal core microbiota where topologically distinct co-occurrence networks were constructed for the adjacent luminal and mucosal compartments. When comparing the GI microbiota from different hosts, we found that the rat microbial biogeography might represent a new reference, distinct from other murine animals. Our study provides the first comprehensive characterization of the rat GI microbiota landscape for the research community, laying the foundation for better understanding and predicting the disease-related alterations in microbial communities.

In a previous study, we uncovered three immune-responsive patterns of gut microbes using an in vitro mesenteric lymph node cell suspension model, abbreviated as the MLN model hereafter. We used Akkermansia muciniphila and Clostridium butyricum as the first group directly inducing an immune response, Bifidobacterium sp. and Bacteroides sp. as the second group evoking an immune response with the help of stimuli (anti-CD3 and anti-CD28 antibodies), and Lactobacillus sp. as the third group blunting the immune response with or without stimuli. Our group previously clarified the immune-activation characteristics of A. muciniphila and linked its in vivo immune induction effect in GF and SPF mice under homeostasis. In the present study, we supplemented the characteristics of C. butyricum and B. bifidum in the in vitro MLN model and addressed the specific elements of the model. Finally, we used an in vivo TNBS-challenge model to show the functional differences between these species with different response patterns in vitro. The results showed that C. butyricum and B. bifidum evoked an immune response in vitro in a dose-dependent and strain-unique manner. Although TLR2, rather than TLR4, is indispensable for immune activation in the present in vitro model, it may not involve interaction between TLR2 and bacterial ligands. Like the PBMC model, the present in vitro MLN model is highly dependent on cell resources and should be given more attention when used to conduct a quantitative comparison. Finally, a mixture of two strong immunogenic strains, A. muciniphila and C. butyricum, significantly increased the mortality of TNBS-challenged (2,4,6-trinitrobenzene sulfonic acid, TNBS) mice, indicating a possible link between the in vitro MLN model and in vivo functional evaluation. However, more evidence is needed to clarify the associations and underlying mechanisms.

There is mounting evidence that the microbiota-gut-brain axis (MGBA) is critical in the pathogenesis and progression of Parkinson's disease (PD), suggesting that probiotic therapy restoring gut microecology may slow down disease progression. In this study, we examined the disease-alleviating effects of Bifidobacterium breve CCFM1067, orally administered for 5 weeks in a PD mouse model. Our study shows that supplementation with the probiotic B. breve CCFM1067 protected dopaminergic neurons and suppressed glial cell hyperactivation and neuroinflammation in PD mice. In addition, the antioxidant capacity of the central nervous system was enhanced and oxidative stress was alleviated. Moreover, B. breve CCFM1067 protected the blood-brain and intestinal barriers from damage in the MPTP-induced mouse model. The results of fecal microbiota analysis showed that B. breve CCFM1067 intervention could act on the MPTP-induced microecological imbalance in the intestinal microbiota, suppressing the number of pathogenic bacteria (Escherichia-Shigella) while increasing the number of beneficial bacteria (Bifidobacterium and Akkermansia) in PD mice. In addition, the increase in short chain fatty acids (acetic and butyric acids) may explain the anti-inflammatory action of B. breve CCFM1067 in the gut or brain of the MPTP-induced PD mouse model. In conclusion, we demonstrated that the probiotic B. breve CCFM1067, which can prevent or treat PD by modulating the gut-brain axis, can be utilized as a possible new oral supplement for PD therapy.

The occurrence of non-alcoholic fatty liver disease (NAFLD) is closely related to intestinal microbiota disturbance, and probiotics has become a new strategy to assist in alleviating NAFLD. In order to investigate the effect of Bifidobacterium on NAFLD and the possible pathway, a NAFLD model was established by using a high-fat diet (HFD) for 18 weeks. Fourteen strains of Bifidobacterium were selected (seven Bifidobacterium adolescentis and seven Bifidobacterium bifidum) for intervention. The effects of different bifidobacteria on NAFLD were evaluated from liver cell injury, liver fat deposition, liver inflammatory state and liver histopathology, and were taken as entry points to explore the mitigation approaches of bifidobacteria through energy intake, lipid metabolism, glucose metabolism and intestinal permeability. The results showed that Bifidobacterium exerts species-specific effects on NAFLD. B. bifidum exerted these effects mainly through regulating the intestinal microbiota, increasing the relative abundance of Faecalibaculum and Lactobacillus, decreasing the relative abundance of Tyzzerella, Escherichia-Shigella, Intestinimonas, Osillibacter and Ruminiclostridium, and further increasing the contents of propionic acid and butyric acid, regulating lipid metabolism and intestinal permeability, and ultimately inhibiting liver inflammation and fat accumulation to alleviate NAFLD. B. adolescentis exerted its effects mainly through changing the intestinal microbiota, increasing the content of propionic acid, regulating lipid metabolism and ultimately inhibiting liver inflammation to alleviate NAFLD.

Increasing attention has been paid to the potential probiotic effects of Latilactobacillus sakei. To explore the genetic diversity of L. sakei, 14 strains isolated from different niches (feces, fermented kimchi, and meat products) and 54 published strains were compared and analyzed. The results showed that the average genome size and GC content of L. sakei were 1.98 Mb and 41.22%, respectively. Its core genome mainly encodes translation and transcription, amino acid synthesis, glucose metabolism, and defense functions. L. sakei has open pan-genomic characteristics, and its pan-gene curve shows an upward trend. The genetic diversity of L. sakei is mainly reflected in carbohydrate utilization, antibiotic tolerance, and immune/competition-related factors, such as clustering regular interval short palindromic repeat sequence (CRISPR)-Cas. The CRISPR system is mainly IIA type, and a few are IIC types. This work provides a basis for the study of this species.

Aluminum contamination of water is becoming increasingly serious and threatens the health status of fish. Lactobacillus plantarum CCFM639 was previously shown to be a potential probiotic for alleviation aluminum toxicity in Nile tilapia. Considering the significant role of the gut microbiota on fish health, it seems appropriate to explore the relationships among aluminum exposure, probiotic supplementation, and the gut microbiota in Nile tilapia and to determine whether regulation of the gut microbiota is related to alleviation of aluminum toxicity by a probiotic in Nile tilapia.

Autism spectrum disorder (ASD) is a neuro-developmental disorder that is characterized by impairments of reciprocal social interaction and restricted stereotyped repetitive behavior. The goal of the present study was to investigate the trace element and gut microbiota profiles of Chinese autistic children and screen out potential metallic or microbial indicators of the disease. One hundred and thirty-six children (78 with ASD and 58 healthy controls) aged from 3 to 7 years were enrolled. The levels of lead, cadmium, arsenic, copper, zinc, iron, mercury, calcium and magnesium in hair samples from the children were analyzed. Fecal samples were also collected and the children's gut microbiota profiles were characterized by 16s rRNA sequencing. Concentrations of lead, arsenic, copper, zinc, mercury, calcium and magnesium were significantly higher in the ASD group than in the control group. Linear discriminant analysis effect size analysis indicated that the relative abundance of nine genera was increased in the autistic children. Redundancy analysis showed that arsenic and mercury were significantly associated with Parabacteroides and Oscillospira in the gut. A random forest model was trained with high accuracy (84.00%) and the metallic and microbial biomarkers of ASD were established. Our results indicate significant alterations in the trace element and gut microbiota profiles of Chinese children with ASD and reveal the potential pathogenesis of this disease in terms of metal metabolism and gut microecology.

Adhesion to epithelial cells is considered important for Lactobacillus to exert probiotic effects. In this study, we found that trypsin treatment decreased the adhesion ability of Lactobacillus plantarum AR326 and AR269, which exhibit good adhesion ability, and surface proteins extracts increased the adhesion of the strains with poor adhesion ability. By SDS-polyacrylamide gel electrophoresis and mass spectrometry analysis, the main component of the surface proteins was detected and identified as a protein of approximately 37 kDa. It was 100% homologous with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from L. plantarum WCFS1. The adhesion of AR326 and AR269 was decreased significantly by blocking with the anti-GAPDH antibody, and GAPDH restored the adhesion of AR326 and AR269 treated with trypsin. In addition, purified GAPDH significantly increased the adhesion of the strains with poor adhesion ability. These results indicated that GAPDH mediates the adhesion of these highly adhesive lactobacilli to epithelial cells and can be used to improve the adhesion ability of probiotics or other bacteria of interest.

A whole-bacterium-based SELEX (Systematic Evolution of Ligands by Exponential Enrichment) procedure was adopted in this study for the selection of an ssDNA aptamer that binds to Bifidobacterium bifidum. After 12 rounds of selection targeted against B. bifidum, 30 sequences were obtained and divided into seven families according to primary sequence homology and similarity of secondary structure. Four FAM (fluorescein amidite) labeled aptamer sequences from different families were selected for further characterization by flow cytometric analysis. The results reveal that the aptamer sequence CCFM641-5 demonstrated high-affinity and specificity for B. bifidum compared with the other sequences tested, and the estimated Kd value was 10.69 ± 0.89 nM. Additionally, sequence truncation experiments of the aptamer CCFM641-5 led to the conclusion that the 5'-primer and 3'-primer binding sites were essential for aptamer-target binding. In addition, the possible component of the target B. bifidum, bound by the aptamer CCFM641-5, was identified as a membrane protein by treatment with proteinase. Furthermore, to prove the potential application of the aptamer CCFM641-5, a colorimetric bioassay of the sandwich-type structure was used to detect B. bifidum. The assay had a linear range of 10⁴ to 10⁷ cfu/mL (R² = 0.9834). Therefore, the colorimetric bioassay appears to be a promising method for the detection of B. bifidum based on the aptamer CCFM641-5.

Aluminum (Al) is toxic to animals and humans. The most common sources of human exposure to Al are food and beverages. The intestinal epithelium is the first barrier against Al-induced toxicity. In this study, HT-29, a human colon cancer cell line, was selected as an in vitro model to evaluate the Al-induced alteration in metabolomic profiles and explore the possible mechanisms of Al toxicity.

Cadmium (Cd) is a toxic metal inducing a range of adverse effects on organs including liver and kidneys. However, the underlying molecular mechanisms of Cd-induced intestinal toxicity through dietary intake is poorly studied. This study evaluated the toxic effects of Cd on intestinal physiology and confirmed the effectiveness of the protective mechanism of the probiotic Lactobacillus plantarum CCFM8610 against chronic Cd toxicity. After treatment with Cd, the HT-29 cell line was subjected to iTRAQ analysis, which revealed that changes in the proteomic profiles after Cd exposure were related to pathways involved in the stress response and carbohydrate metabolism. The results of an animal trial also indicated that 10 weeks of Cd exposure decreased the fecal water content and contractile response of colonic muscle strips in mice, and delayed the excretion time of the first black feces. L. plantarum CCFM8610 treatment provided protective effects against these Cd-induced intestinal motility dysfunctions by recovering the levels of neurotransmitters, including substance P, acetyl cholinesterase, vasoactive intestinal peptide, 5-hydroxytryptamine, calcitonin gene-related peptide, and nitric oxide, and suppressing the cellular stress response in mice (e.g., the inhibition of mitogen-activated protein kinase pathways). The administration of this probiotic was also observed to reduce Cd levels in the tissues and blood of the mice. Our results suggest a newly identified protective mechanism of probiotics against Cd toxicity that involves the recovery of intestinal motility and increase in fecal cadmium excretion.

Biofilm formation by bacteria represents an adaptation strategy to the environment, and some special genes may lead to a strong biofilm phenotype. In this study, we attempted to find functional genes associated with bifidobacterial biofilm formation. Firstly, we evaluated the biofilm formation ability of bifidobacterial strains from six species, which showed that Bifidobacterium longum, Bifidobacterium breve, Bifidobacterium animalis, Bifidobacterium adolescentis, and Bifidobacterium pseudocatenulatum had biofilm-forming and non-biofilm-forming strains, while all Bifidobacterium bifidum strains could form strong biofilms. Then 48 strains were selected for genome sequencing and comparative analysis. The gene-trait matching analysis revealed that B. bifidum biofilm formation phenotype may associate with their unique genes, involving in stress response, quorum sensing, two components, and peptide synthesis. B. pseudocatenulatum biofilm formation was positively correlated with the eps cluster (rfbX). While no genotype related to the biofilm phenotype was found in B. longum using this analysis, but all contain autoinducer-2 (AI-2) receptor genes. Moreover, luxS, rbsB, rfbX were selected for real-time qPCR analysis, suggesting that their expression are important to biofilm formation. These results indicated that strains carrying certain genes tend to form stronger biofilms than those formed by strains without these genes.

Aluminum (Al) is a ubiquitous metal that can seriously harm the health of animals and humans. In our previous study, we demonstrated that Lactobacillus plantarum CCFM639 can decrease Al burden in the tissues of mice by inhibiting intestinal Al absorption. The main aim of the present research was to investigate whether the protection by the strain is also associated with enhancement of the intestinal barrier, alleviation of oxidative stress and modulation of the inflammatory response. In an in vitro cell model, two protection modes (intervention and therapy) were examined and the results indicated that L. plantarum CCFM639 alleviated Al-induced cytotoxicity. In a mouse model, L. plantarum CCFM639 treatment was found to significantly alleviate oxidative stress in the intestinal tract, regulate the function of the intestinal mucosal immune system, restore the integrity of tight junction proteins and maintain intestinal permeability. These results suggest that in addition to Al sequestration, L. plantarum CCFM639 can also inhibit Al absorption by protecting the intestinal barrier, alleviating Al-induced oxidative stress and inflammatory response. Therefore, L. plantarum CCFM639 has the potential to be a dietary supplement ingredient that provides protection against Al-induced gut injury.

Constipation is one of the most common gastrointestinal complaints worldwide. This study was performed to determine whether Bifidobacterium adolescentis exerts inter-strain differences in alleviating constipation induced by loperamide in BALB/c mice and to analyze the main reasons for these differences. BALB/c mice underwent gavage with B. adolescentis (CCFM 626, 667, and 669) once per day for 17 days. The primary outcome measures included related constipation indicators, and the secondary outcome measures were the basic biological characteristics of the strains, the concentration changes of short-chain fatty acids in feces, and the changes in the fecal flora. B. adolescentis CCFM 669 and 667 relieved constipation symptoms by adhering to intestinal epithelial cells, growing quickly in vitro and increasing the concentrations of propionic and butyric acids. The effect of B. adolescentis on the gut microbiota in mice with constipation was investigated via 16S rRNA metagenomic analysis. The results revealed that the relative abundance of Lactobacillus increased and the amount of Clostridium decreased in the B. adolescentis CCFM 669 and 667 treatment groups. In conclusion, B. adolescentis exhibits strain-specific effects in the alleviation of constipation, mostly due to the strains' growth rates, adhesive capacity and effects on the gut microbiome and microenvironment.

Constipation is a prevalent gastrointestinal disorder that seriously reduces the quality of life. Clinical studies have shown that a great change or severe imbalance occurs in the intestinal microbiota of people with constipation. This study explored whether bacteriocin-producing and non-bacteriocin-producing Pediococcus acidilactici strains resulted in differences in the alleviation of constipation and changes in the fecal flora in BALB/c mice. The constipation-related indicators, gastrointestinal regulatory peptides and gut microbiota were identified to evaluate their alleviating effects and underlying mechanisms. The time to the first black-stool defecation and the gastrointestinal transit rate in constipated mice were found to be somewhat improved by four P. acidilactici strains (P > 0.05). Moreover, there were significant differences in the level of most gastrointestinal regulatory peptides in the serum, as well as in the composition and abundance of intestinal microbiota in different groups (P < 0.05). At the phylum level, the relative abundance of Firmicutes was significantly increased, but those of Bacteroidetes and Proteobacteria were significantly reduced after the administration of four P. acidilactici strains for 14 d (P < 0.05). The levels of Bacteroides and genera from Enterobacteriaceae were significantly decreased, whereas Bifidobacterium and Lactobacillus were upregulated when bacteriocin-producing P. acidilactici CCFM18 and CCFM28 strains were provided in the diet (P < 0.05). The results indicated that although constipation-related symptoms were alleviated to only a limited degree, the administration of four P. acidilactici strains effectively regulated the gut flora and provided a potential health benefit to the host, especially the bacteriocin-producing P. acidilactici strains.