Correction: Administering Lactiplantibacillus fermentum F6 decreases intestinal Akkermansia muciniphila in a dextran sulfate sodium-induced rat colitis model.

Correction for 'Administering Lactiplantibacillus fermentum F6 decreases intestinal Akkermansia muciniphila in a dextran sulfate sodium-induced rat colitis model' by Qiuwen He et al., Food Funct., 2024, 15, 5882-5894, https://doi.org/10.1039/d4fo00462k.

Administering Lactiplantibacillus fermentum F6 decreases intestinal Akkermansia muciniphila in a dextran sulfate sodium-induced rat colitis model.

Probiotics are increasingly used to manage gut dysbiosis-related conditions due to their robust ability to manipulate the gut microbial community. However, few studies have reported that probiotics can specifically modulate individual gut microbes. This study demonstrated that administering the probiotic, Lactiplantibacillus fermentum F6, could ameliorate dextran sulfate sodium-induced colitis in a rat model, evidenced by the decreases in the disease activity index score, histopathology grading, and serum pro-inflammatory cytokine levels, as well as the increase in the serum anti-inflammatory cytokine levels. Shotgun metagenomics revealed that the fecal metagenomic of colitis rats receiving the probiotic intervention contained substantially fewer Akkermansia muciniphila than the dextran sulfate sodium group. Thus, the probiotic mechanism might be exerted by reducing specific gut microbial species associated with disease pathogenesis. A new paradigm for designing probiotics that manage diseases through direct and precise manipulation of gut microbes has been provided through this study.

Preliminary Purification and Partial Characterization of a Functional Bacteriocin of Lacticaseibacillus paracasei Zhang and Mining for its Gene Cluster.

Bacteriocins produced by lactic acid bacteria (LAB) have good potential for use as food biopreservatives. Lacticaseibacillus paracasei Zhang (L. paracasei Zhang) is both a food use and a probiotic bacterium. This study aimed to purify and preliminary characterize the active antibacterial metabolite of L. paracasei Zhang. The cell-free supernatant of L. paracasei Zhang was collected and purified by ultrafiltration and gel filtration chromatography. The 1-3 kDa active fraction could inhibit the growth of Staphylococcus aureus but not Escherichia coli. Further antibacterial activity assays revealed its capacity to suppress various foodborne and human opportunistic pathogens (including Staphylococcus aureus, Pseudomonas fluorescens, Pseudomonas aeruginosa, Listeria monocytogenes, and Bacillus cereus), but not fungi. The antibacterial activity showed good tolerance to heat (40 to 100 °C), acid-base (pH 2-3 and pH 6-10), and digestions by a number of industrial and animal/human enzymes (such as trypsin, pepsin, α-amylase, and protease K, except papain); these desired properties make it a suitable biopreservative to be used in harsh and complex industrial production processes. The high papain sensitivity suggested a proteinaceous/peptide nature of the bioactivity. Moreover, our genomic data mining for bacteriocin through BAGEL4 revealed an area of interest encoding a complete set of putative genes required for bacteriocin production. In conclusion, our study showed that L. paracasei Zhang can produce extracellular functional antibacterial metabolite, likely a class II bacteriocin. Our preliminary extraction and characterization of the active metabolite demonstrated that it has good potential to be used as a biopreservative or an agent for suppressing gastrointestinal infections.

Both viable Bifidobacterium longum subsp. infantis B8762 and heat-killed cells alleviate the intestinal inflammation of DSS-induced IBD rats.

In view of the safety concerns of probiotics, more and more attention is paid to the beneficial effects of dead probiotics cells. Herein, we investigated and compared the alleviation effects of viable Bifidobacterium longum subsp. infantis B8762 (B. infantis B8762) and its heat-killed cells on dextran sodium sulfate (DSS)-induced inflammatory bowel disease (IBD) rats. Four groups of rats (n = 12 per group) were included: normal control, DSS-induced colitis rats without bacterial administration (DSS), DSS-induced colitis rats with viable B. infantis B8762 administration (VB8762), and DSS-induced colitis rats with dead B. infantis B8762 administration (DB8762). Our results showed that both VB8762 and DB8762 administration exerted significant protective effects on DSS-induced IBD rats, as evidenced by a reduction in mortality, disease activity index score, body weight loss, as well as decreased histology score, which were companied by a significant decrease in serum pro-inflammatory factors compared with DSS group, and a stronger effect on modulating the fecal microbiota alpha-diversity and beta-diversity compared with DSS group. Additionally, the fecal metabolome results showed that both VB8762 and DB8762 interventions indeed altered the fecal metabolome profile and related metabolic pathways of DSS-induced IBD rats. Therefore, given the alleviation effects on colitis, the DB8762 can be confirmed to be a postbiotic. Overall, our findings suggested that VB8762 and DB8762 had similar ability to alleviate IBD although with some differences. Due to the minimal safety concern of postbiotics, we propose that the postbiotic DB8762 could be a promising alternative to probiotics to be applied in the prevention and treatment of IBDs.IMPORTANCEInflammatory bowel disease (IBD) has emerged as a global disease because of the worldwide spread of western diets and lifestyles during industrialization. Up to now, many probiotic strains are used as a modulator of gut microbiota or an enhancer of gut barrier to alleviate or cure IBD. However, there are still many issues of using probiotics, which were needed to be concerned about, for instance, safety issues in certain groups like neonates and vulnerable populations, and the functional differences between viable and dead microorganisms. Therefore, it is of interest to investigate the beneficial effects of dead probiotics cells. The present study proved that both viable Bifidobacterium longum subsp. infantis B8762 and heat-killed cells could alleviate dextran sodium sulfate-induced colitis in rats. The findings help to support that some heat-killed probiotics cells can also exert relevant biological functions and can be used as a postbiotic.

Dynamic Changes of the Gut Microbiota and Its Functional Metagenomic Potential during the Development of Non-Small Cell Lung Cancer.

The gut microbiota plays a significant role in tumor pathogenesis by regulating the host metabolism and immune response, and there are few studies focused on tracking changes in the gut microbiota from the onset of lung cancer. Therefore, the aim of our study is combining preclinical and clinical research to thoroughly analyze the signatures of fecal microbiota in lung cancer, which will be useful for early diagnosis and predicting the therapeutic efficacy of lung cancer. The first part of this study analyzed the fecal metagenomic differences between patients with non-small cell lung cancer and healthy subjects, and the second part of this work constructed a murine lung cancer model to monitor changes in mouse fecal metagenomics and T cell immunology during lung cancer progression. We found that the fecal microbiota was altered in both humans and mice with lung cancer, characterized by a significantly reduced microbial diversity and number of beneficial microbes, with increases in potential pathogens. The fecal level of Akkermansia muciniphila and the gut metabolic module of the secondary bile acid metabolism were diminished in both humans and mice with lung cancer compared with healthy subjects. Splenomegaly was observed in the lung cancer mice. Flow cytometer analysis of the splenocytes revealed substantial alterations in the proportions of T cell subsets in the lung cancer mice, characterized by significant increases in CD4+Foxp3+CD25+ T regulatory cells (p < 0.05) while significant decreases in CD3+ T cells (p < 0.001), CD4+ T cells (p < 0.001), and the CD4+/CD8+ ratio (p < 0.01). Vertical and longitudinal analyses of the fecal microbiota of the two mouse groups identified some lung cancer biomarkers (including Acutalibacter timonensis, Lachnospiraceae bacterium NSJ-38 sp014337195, etc.). The fecal microbiota of the lung cancer mice had a reduced metagenomic potential for neurotransmitters (melatonin, γ-aminobutyric acid, and histamine) compared with healthy mice. In summary, this study found that the diversity, structure, and composition of gut microbiota vary between cancer and healthy conditions, ultimately leading to changes in the potential for functional metagenomics.

Postbiotic Administration Ameliorates Colitis and Inflammation in Rats Possibly through Gut Microbiota Modulation.

Postbiotics are preparations of inanimate microorganisms and/or their components that are beneficial to host health. Compared with probiotics, the postbiotic dose required for exerting obvious protective effects is unknown. Thus, we conducted a dose-dependent postbiotic intervention study in dextran sulfate sodium (DSS)-induced colitis rats. The trial included five rat groups, including: control without DSS/postbiotic treatment, group C; 7-day DSS treatment, group D; 14-day low, medium, and high probiotic doses (0.1, 0.2, 0.4 g/kg; groups L, M, H, respectively) after DSS induction. We found that postbiotic intervention effectively mitigated the symptoms and inflammation in colitis rats, evidenced by the improved spleen index, less severe colon tissue damage, and changes in serum cytokine levels (decreases in tumor necrosis factor-α and interleukin-1ß; increase in interleukin-10) in postbiotic groups compared with group D. Moreover, the therapeutic effect was dose-dependent. Fecal metabolomics analysis revealed that the postbiotic recipients had more anti-inflammatory metabolites, namely, salicyloyl phytophingosine, podophylloxin, securinine, baicalein, and diosmetin. Fecal metagenomics analysis revealed that the postbiotic recipients had more beneficial microbes and less pro-inflammatory bacteria. This study confirmed that postbiotics are effective in alleviating colitis in a dose-dependent manner. Our findings are of interest to food scientists, clinicians, and the health food industry.

A co-type ductile film with high tensile strength and fast self-healing properties for shaped fruit preservation.

Traditional petroleum-based plastics have high energy consumption, require professional equipment, are non-degradable after use, and lack antibacterial properties, making it impossible to achieve long-lasting freshness in fruits and vegetables. Herein, we report a novel co-type film-forming method with low energy consumption and without production equipment, which uses PVA-borax gel as a substrate and adds a certain proportion of CMC and TA to prepare multifunctional CMC/TA@PVA-borax composite hydrogels (CTPB). The dynamic borax ester bonding and hydrogen bonding in the CTPB hydrogel results in an ultra-high tensile strength of more than 5500% and rapid self-healing within 8 s. Interestingly, hydrogels can be arbitrarily shaped and stretched like play dough and thus can be stretched into ductile films by co-type film formation. The antimicrobial properties of the hydrogel film can be attributed to the synergistic effects of TA and borax. The mussel structure of TA allows the hydrogel film to adhere directly to different surfaces for more effective bacterial killing. In addition, the hydrogel film has a high level of biosafety and biodegradability and shows good performance in fruit storage. This study provides a convenient and low-energy method for the preparation of films, which in part reduces the increasing environmental pollution caused by petroleum-based plastics.

A high-quality genome compendium of the human gut microbiome of Inner Mongolians.

Metagenome-based resources have revealed the diversity and function of the human gut microbiome, but further understanding is limited by insufficient genome quality and a lack of samples from typically understudied populations. Here we used hybrid long-read PromethION and short-read HiSeq sequencing to characterize the faecal microbiota of 60 Inner Mongolian individuals (n = 180 samples over three time points) who were part of a probiotic yogurt intervention trial. We present the Inner Mongolian Gut Genome catalogue, comprising 802 closed and 5,927 high-quality metagenome-assembled genomes. This approach achieved high genome continuity and substantially increased the resolution of genomic elements, including ribosomal RNA operons, metabolic gene clusters, prophages and insertion sequences. Particularly, we report the ribosomal RNA operon copy numbers for uncultured species, over 12,000 previously undescribed gut prophages and the distribution of insertion sequence elements across gut bacteria. Overall, these data provide a high-quality, large-scale resource for studying the human gut microbiota.

Heat-Killed Bifidobacterium bifidum B1628 May Alleviate Dextran Sulfate Sodium-Induced Colitis in Mice, and the Anti-Inflammatory Effect Is Associated with Gut Microbiota Modulation.

Inflammatory bowel disease (IBD) is a chronic inflammatory disease associated with gut dysbiosis. This study aimed to investigate the effects of heat-killed Bifidobacterium bifidum B1628 (HB1628) in dextran sulfate sodium (DSS)-induced colitis in mice. The following three mouse groups were included (n = eight per group): NC (normal control), DSS (colitis), and HB1628 (colitis and postbiotic). The mice in the DSS group showed significant weight loss and histological damage, developed bloody diarrhea, scored high in the disease activity index (DAI), and exhibited increases in pro-inflammatory cytokines (interleukin [IL]-1ß, IL-6, and tumor necrosis factor [TNF]-α) and decreases in an anti-inflammatory cytokine (IL-13) in the serum. These changes were accompanied by gut microbiota modulation in colitis mice (decreases in Rikenellaceae and Eubacterium; increases in Peptostreptococcaceae, Bacteroides vulgatus, and Parasutterella excrementihominis). The HB1628 group had lower DAIs, histology scores, and serum levels of pro-inflammatory cytokines (IL-1ß and TNF-α), but higher levels of an anti-inflammatory cytokine (IL-13), compared with the DSS group, suggesting a less severe inflammatory state after the HB1628 intervention. Additionally, HB1628 improved DSS-induced gut dysbiosis, which is evidenced by increases in intestinal beneficial bacteria, such as Lactobacillus, and decreases in known unfavorable taxa in IBD, e.g., Porphyromonadaceae, Subdoligranulum, Lachnospiraceae bacterium 3_1_46FAA, and Alistipes indistinctus. Functional metagenomics revealed three significantly enriched metabolic pathways in the HB1628 group (namely, the aerobic respiration I [cytochrome c] pathway and the superpathways of L-phenylalanine biosynthesis and L-tryptophan biosynthesis, respectively). In conclusion, our results showed that HB1628 effectively improved the inflammation state and tissue damage in DSS-induced colitis mice, and the symptom relief effect was accompanied by obvious gut microbiota remodulation.

Stronger gut microbiome modulatory effects by postbiotics than probiotics in a mouse colitis model.

Probiotics are increasingly used as adjunctive therapy to manage gastrointestinal diseases, such as ulcerative colitis. However, probiotic use has posed some safety concerns. Thus, postbiotics are proposed as alternatives to probiotics in clinical applications. However, no study has directly compared the clinical benefits of probiotics and postbiotics. This study compared the beneficial effect of postbiotics and probiotics derived from the strain, Bifidobacterium adolescentis B8598, in a dextran sulfate sodium (DSS)-induced experimental colitis mouse model. Four groups of mice (n = 7 per group) were included in this work: Control (received water plus saline), DSS (received DSS without postbiotic/probiotic), Postbiotic (received DSS plus postbiotic), and Probiotic (received DSS plus probiotic). Our results showed that intragastric administration of both probiotic and postbiotic ameliorated colitis, reflected by decreased histology scores in Postbiotic and Probiotic groups compared with DSS group (P < 0.05). The fecal microbiota alpha diversity was not significantly affected by DSS-, postbiotic, or probiotic treatment. However, the postbiotic treatment showed stronger effects on modulating the fecal microbiota beta diversity, composition, and metagenomic potential than the probiotic treatment. Overall, our findings suggested that probiotics and postbiotics had similar ability to improve disease phenotype but had distinct ability to regulate the gut microbiota and metabolic pathways in the context of ulcerative colitis. In view of the smaller safety concern of postbiotics compared with probiotics and its stronger modulatory effect on the host gut microbiota, we propose that postbiotics are to be considered for use as next-generation biotherapeutics in managing ulcerative colitis or even other diseases.

The Lactobacillus gasseri G098 Strain Mitigates Symptoms of DSS-Induced Inflammatory Bowel Disease in Mice.

Inflammatory bowel disease (IBD) is a recurring inflammatory disease of the gastrointestinal tract with unclear etiology, but it is thought to be related to factors like immune abnormalities and gut microbial dysbiosis. Probiotics can regulate host immunity and gut microbiota; thus, we investigated the alleviation effect and mechanism of the strain Lactobacillus gasseri G098 (G098) on dextran sodium sulfate (DSS)-induced colitis in mice. Three groups of mice (n = 8 per group) were included: normal control (NC), DSS-induced colitis mice (DSS), and colitis mice given strain (G098). Our results showed that administering G098 effectively reversed DSS-induced colitis-associated symptoms (mitigating weight loss, reducing disease activity index and pathology scores; p < 0.05 in all cases) and prevented DSS-induced mortality (62.5% in DSS group; 100% in G098 group). The mortality rate and symptom improvement by G098 administration was accompanied by a healthier serum cytokine balance (significant decreases in serum pro-inflammatory factors, interleukin (IL)-6 [p < 0.05], IL-1ß [p < 0.01], and tumor necrosis factor (TNF)-α [p < 0.001], and significant increase in the serum anti-inflammatory factor IL-13 [p < 0.01], compared with DSS group) and gut microbiome modulation (characterized by a higher gut microbiota diversity [p < 0.05], significantly more Firmicutes and Lachnoclostridium [p < 0.05], significantly fewer Bacteroidetes [p < 0.05], and significant higher gene abundances of sugar degradation-related pathways [p < 0.05], compared with DSS-treated group). Taken altogether, our results suggested that G098 intake could mitigate DSS-induced colitis through modulating host immunity and gut microbiome, and strain treatment is a promising strategy for managing IBD.

Factors Associated with Outpatient Satisfaction in Provincial Tertiary Hospitals in Nanchang, China: A Structural Equation Modeling Approach.

Outpatient satisfaction is important in evaluating the performance of tertiary public hospitals in China. However, only a few studies have examined the interaction between outpatient satisfaction and its related factors. This study aimed to explore the relationship between patient satisfaction and its related factors in provincial tertiary hospitals. Six hundred outpatients in three provincial tertiary hospitals in Nanchang, China, were randomly selected. Structural equation modeling was used to analyze the relationship of the factors associated with outpatient satisfaction. The conceptual model fitted the data well (χ2/df = 4.367, CFI = 0.951, TLI = 0.937, SRMR = 0.055, RMSEA = 0.075), with all the path coefficients being statistically significant (p < 0.001). The environment and facilities showed the most significant influence on outpatient satisfaction (standardized total effect = 0.389), followed by the quality of diagnosis and treatment (standardized total effect = 0.235). The waiting time for medical services showed a partial mediation effect of 0.077 between the environment and facilities and outpatient satisfaction. The study indicates that targeted measures should be taken to improve the amenities of hospitals and shorten the waiting time for medical services, thus further improving outpatients' medical experience.

Lactobacillus casei Zhang exerts anti-obesity effect to obese glut1 and gut-specific-glut1 knockout mice via gut microbiota modulation mediated different metagenomic pathways.

PURPOSE: Obesity is a major risk factor for various metabolic diseases, including metabolic syndrome and type-2 diabetes. Glucose transporter 1 (GLUT1) impairment has been proposed as a mechanism of fat accumulation and glucose tolerance. Our aims were to determine the role of intestinal epithelial glut1 activity in obesity and the mechanism of anti-obesity effect of Lactobacillus casei Zhang (LCZ) intervention in the absence of gut villi-specific glut1 expression. METHODS: This study compared the body weight, intestinal microbiota perturbations, fat mass accumulation, and glucose tolerance (by oral glucose tolerance test) between high-fat diet fed villi-specific glut1 knockout (KO) mice and control mice (glut1 flox/flox) with/without LCZ intervention. The intestinal microbiota was evaluated by metagenomic sequencing. RESULTS: Our results showed that villi-specific glut1 KO mice had more fat deposition at the premetaphase stage, impaired glucose tolerance, and obvious alterations in gut microbiota compared to control mice. Probiotic administration significantly lowered the body weight, the weights of mesenteric and perirenal white adipose tissues (WAT), and mediated gut microbiota modulation in both types of KO and control mice. The species Barnesiella intestinihominis and Faecalibaculum rodentium might contribute to fasting fat mass accumulation associated with gut-specific glut1 inactivation, while the probiotic-mediated anti-obesity effect was linked to members of the Bacteroides genera, Odoribacter genera and Alistipes finegoldii. CONCLUSION: Our study demonstrated that abrogating gut epithelial GLUT1 activity affected the gut microbiota, fat mass accumulation, and glucose tolerance; and LCZ administration reduced fat mass accumulation and central obesity.

Intake of Bifidobacterium lactis Probio-M8 fermented milk protects against alcoholic liver disease.

Alcoholic liver disease (ALD) is a liver disease caused by long-term heavy drinking, which is characterized by increased inflammation and oxidative stress in the liver and gut dysbiosis. The purpose of this study was to investigate the protective effect of administering ordinary and probiotic- (containing the Bifidobacterium animalis ssp. lactis Probio-M8 strain; M8) fermented milk to rats. Several biochemical parameters and the fecal metagenomes were monitored before (d 0) and after (d 42) the intervention. Our results confirmed that alcohol could cause significant changes in the liver levels of the proinflammatory cytokine IL-1ß, antioxidation indicators, and liver function-related indicators; meanwhile, the gut bacterial and viral microbiota were disrupted with significant reduction in microbial diversity and richness. Feeding the rats with Probio-M8-fermented milk effectively maintained the gut microbiota stability, reduced liver inflammation and oxidative stress, and mitigated liver damages in ALD. Moreover, the Probio-M8-fermented milk reversed alcohol-induced dysbiosis by restoring the gut microbiota diversity, richness, and composition. Four predicted fecal metabolites (inositol, tryptophan, cortisol, and vitamin K2) increased after the intervention, which might help regulate liver metabolism and alleviate ALD-related symptoms. In short, our data supported that consuming Probio-M8-fermented milk effectively mitigated ALD. The protective effect against ALD could be related to changes in the gut microbiome after probiotic-fermented milk consumption. However, such observation and the causal relationship among probiotic milk consumption, changes in gut microbiome, and disease alleviation would still need to be further confirmed. Nevertheless, this study has shown in a rat model that consuming probiotic-fermented milk could protect against ALD.

Treatment with mixed probiotics induced, enhanced and diversified modulation of the gut microbiome of healthy rats.

Previous studies demonstrated that multi-strain probitics could more strongly regulate intestinal cytokines and the mucosal barrier than the individual ingredient strains. Nevertheless, the potentially different gut microbiome modulation effects between multi-strain and single-strain probiotics treatments remain unexplored. Here, we administered three different Lactiplantibacillus plantarum strains or their mixture to healthy Wistar rats and compared the shift of gut microbiome among the treatment groups. A 4-week intervention with mixed probiotics induced more drastic and diversified gut microbiome modulation than single-strain probiotics administration (alpha diversity increased 8% and beta diversity increased 18.7%). The three single-strain probiotics treatments all converged the gut microbiota, decreasing between-individual beta diversity by 12.7% on average after the treatment, while multi-strain probiotics treatment diversified the gut microbiome and increased between-individual beta diversity by 37.2% on average. Covariation analysis of the gut microbes suggests that multi-strain probiotics could exert synergistic, modified and enhanced modulation effects on the gut microbiome based on strain-specific modulation effects of probiotics. The more heterogeneous responses to the multi-strain probiotics treatment suggest that future precision microbiome modulation should consider the potential interactions of the probiotic strains, and personalized response to probiotic formulas due to heterogenous gut microbial compositions.

The meconium microbiota shares more features with the amniotic fluid microbiota than the maternal fecal and vaginal microbiota.

The early-life gut microbiota is associated with potential development of diseases in adulthood. The sterile womb paradigm has been challenged by recent reports that revealed the presence of the meconium, amniotic fluid, and placenta microbiome. This study aimed to explore the maternal origin of the microbiota of neonate meconium by using the PacBio single-molecule real-time circular consensus sequencing technology. Such technology could produce high fidelity reads of full-length 16S rRNA genes, improving the sensitivity and specificity of taxonomic profiling. It also reduced the risk of false positives. This study analyzed the full-length 16S rRNA-based microbiota of maternal samples (amniotic fluid, feces, vaginal fluid, saliva) and first-pass meconium of 39 maternal-neonate pairs. Alpha- and beta-diversity analyses revealed sample type-specific microbiota features. Most sample types were dominated by sequences representing different genera (Lactobacillus and Curvibacter in the amniotic fluid and vaginal fluid microbiota; Bacillus and Escherichia/Shigella in the meconium microbiota; Bacteroides and Faecalibacterium in the maternal fecal microbiota; Streptococcus and Prevotella in the maternal saliva microbiota). Moreover, specific operational taxonomic units (OTUs) were identified in all sample types. Dyad analysis revealed common OTUs between the meconium microbiota and microbiota of multiple maternal samples. The meconium microbiota shared more features with the amniotic fluid microbiota than the maternal fecal and vaginal microbiota. Our results strongly suggested that the meconium microbiota was seeded from multiple maternal body sites, and the amniotic fluid microbiota contributed most to the seeding of the meconium microbiota among the investigated maternal body sites.

Comparative genomic analysis of Enterococcus faecalis: insights into their environmental adaptations.

BACKGROUND: Enterococcus faecalis is widely studied as a common gut commensal and a nosocomial pathogen. In fact, Enterococcus faecalis is ubiquitous in nature, and it has been isolated from various niches, including the gastrointestinal tract, faeces, blood, urine, water, and fermented foods (such as dairy products). In order to elucidate the role of habitat in shaping the genome of Enterococcus faecalis, we performed a comparative genomic analysis of 78 strains of various origins. RESULTS: Although no correlation was found between the strain isolation habitat and the phylogeny of Enterococcus faecalis from our whole genome-based phylogenetic analysis, our results revealed some environment-associated features in the analysed Enterococcus faecalis genomes. Significant differences were found in the genome size and the number of predicted open reading frames (ORFs) between strains originated from different environments. In general, strains from water sources had the smallest genome size and the least number of predicted ORFs. We also identified 293 environment-specific genes, some of which might link to the adaptive strategies for survival in particular environments. In addition, the number of antibiotic resistance genes was significantly different between strains isolated from dairy products, water, and blood. Strains isolated from blood had the largest number of antibiotic resistance genes. CONCLUSION: These findings improve our understanding of the role of habitat in shaping the genomes of Enterococcus faecalis.

Genomic Variations in Probiotic Lactobacillus plantarum P-8 in the Human and Rat Gut.

The effects of probiotics on host gastrointestinal health have become an area of particular interest in the field of probiotic research. However, the impact of the host intestinal environment on genomic changes in probiotic organisms remains largely unknown. To investigate, Lactobacillus plantarum P-8, a well-studied probiotic bacterium, was consumed by healthy human volunteers and rats. Then, the persistence and genomic stability of P-8 in the host gut were surveyed. qPCR results revealed that after the consumption of one dose, P-8 could be detected in the host gastrointestinal tract for 4-5 weeks. By contrast, after 4 successive weeks of consumption, P-8 could be detected for up to 17 weeks after consumption ceased. In total, 92 P-8 derived strains were isolated from fecal samples and their genomes were sequenced and analyzed. Comparative genomic analysis detected 19 SNPs, which showed the characteristics of neutral evolution in the core genome. In nearly half of samples (n = 39, 42%), the loss of one to three plasmids was observed. The frequent loss of plasmids indicated reductive evolution in the accessory genome under selection pressure within the gastrointestinal tract. We also observed a 609-bp 23S rRNA homologous fragment that may have been acquired from other species after intake. Our findings offer insight into the complex reactions of probiotics to the gut environment during survival in the host. The in vivo genomic dynamics of L. plantarum P-8 observed in this study will aid the commercial development of probiotics with more stable characteristics.