The first 1000 cultured species of the human gastrointestinal microbiota

Acupuncture ameliorates inflammation by regulating gut microbiota in acute ischemic stroke

Background

Acute ischemic stroke(AIS) is a major life-threatening disease.Some studies have found that AIS may be related to gut flora and immune responses. Acupuncture is used widely in the treatment of AIS. However its relevant mechanism is unclear enough. Therefore, in this study, we wanted to confirm that acupuncture was treating AIS through gut flora and immune response.

Methods

We randomly divided 18 rats into equal three groups, including Sham, Middle Cerebral Artery Occlusion (MCAO) and Acupuncture.Rats in the Acupuncture group for a continuous period of three days after surgery. Neurological deficits were assessed using Longa's method, and detection of intestinal flora by 16s rRNA gene sequencing, determination of SCFAs by gas chromatography-mass spectrometry, detection of HDAC and inflammatory cytokines by elisa assay, detection of Th17 and Treg cells by flow cytometry and, observation of pathological and morphological changes in brain and colon tissues by HE staining.

Results

Acupuncture improved the degree of impaired neurological function in MCAO rats and regulated the type and abundance of intestinal bacteria, increased SCFAs of MCAO rats, decreased HDAC1 and HDAC2, modulated the Th17/Treg imbalance, reduced the level of inflammatory factors in the peripheral blood and altered the pathology of the intestine and brain.

Conclusion

Acupuncture repaired neurologic deficits after AIS and may be associated with an immune-inflammatory response mediated by gut microbiota.

Chemical Synthetic Lethality Screens Identify Selective Drug Combinations against Pseudomonas aeruginosa

The emergence of bacterial ESKAPE pathogens presents a formidable challenge to global health, necessitating the development of innovative strategies for antibiotic discovery. Here, we leverage chemical synthetic lethality to locate therapeutic combinations of small molecules against multidrug-resistant Pseudomonas aeruginosa. Using a transposon screen, we identify PyrD as a target for sensitizing P. aeruginosa to subinhibitory doses of ceftazidime. High-throughput inhibitor screens identify two PyrD inhibitors, nordihydroguaiaretic acid (NDGA) and chlorhexidine (CHX), each of which does not significantly affect growth in isolation but exhibits chemical synthetic lethality when combined with low-dose ceftazidime. Downstream biochemical studies elucidate the mechanism of inhibition by NDGA and CHX. Remarkably, this combination is toxic to P. aeruginosa but leaves commensal bacteria, which are more susceptible to antibiotics, unscathed. Aside from advancing drug combinations that may be explored further in the future, our results offer a new approach for devising potent and specific drug combinations against recalcitrant pathogens.

The Microbiome and Metabolic Dysfunction-Associated Steatotic Liver Disease

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a condition wherein excessive fat accumulates in the liver, leading to inflammation and potential liver damage. In this narrative review, we evaluate the tissue microbiota, how they arise and their constituent microbes, and the role of the intestinal and hepatic microbiota in MASLD. The history of bacteriophages (phages) and their occurrence in the microbiota, their part in the potential causation of MASLD, and conversely, "phage therapy" for antibiotic resistance, obesity, and MASLD, are all described. The microbiota metabolism of bile acids and dietary tryptophan and histidine is defined, together with the impacts of their individual metabolites on MASLD pathogenesis. Both periodontitis and intestinal microbiota dysbiosis may cause MASLD, and how individual microorganisms and their metabolites are involved in these processes is discussed. Novel treatment opportunities for MASLD involving the microbiota exist and include fecal microbiota transplantation, probiotics, prebiotics, synbiotics, tryptophan dietary supplements, intermittent fasting, and phages or their holins and endolysins. Although FDA is yet to approve phage therapy in clinical use, there are multiple FDA-approved clinical trials, and this may represent a new horizon for the future treatment of MASLD.

Soy-based purified ingredient diet affects mouse gut permeability and the microbiome in fragile X mice

Introduction

Gastrointestinal problems including vomiting, reflux, flatulence, diarrhea, constipation and colic are common comorbidities in fragile X syndrome. There is accumulating evidence suggesting that leaky gut syndrome causes neurological phenotypes. Although fragile X messenger ribonucleoprotein is ubiquitously expressed, there is a dearth of knowledge regarding its role outside of the brain including effects on gut dysfunction in fragile X. The aim of this study was to generate novel data on gastrointestinal barrier function and the gut microbiome in response to Fmr1 genotype, sex and diet in mice.

Methods

Fmr1KO male mice and littermate controls in an FVB background were maintained on two purified ingredient diets (AIN-93G with casein protein versus soy protein isolate) versus two standard chows (Teklad 2019 with wheat, corn and yeast protein versus Purina 5015 with wheat, soy, corn, yeast and whey protein sources). Gut permeability was quantified by FITC-dextran levels in blood plasma. The cecal microbiome was identified by 16S rRNA sequencing. In addition, gut permeability was tested in Fmr1KO mice in the C57BL/6 J background maintained on casein- and soy protein isolate-based AIN-93G versus Teklad 2019.

Results

Knockout of the Fmr1 gene in FVB mice did not affect gut permeability. Soy protein isolate-based AIN-93G increased gut permeability. Beta-diversity of the cecal microbiome was significantly altered as a function of the four test diets. Akkermansia_muciniphila was increased in Fmr1KO mice fed AIN-93G while unnamed species within the genus Anaerovorax and family Ruminococcaceae were increased and the order Clostridales decreased in Fmr1KO mice fed AIN-93G/soy. Fmr1KO mice in the C57BL/6 J background exhibited increased gut permeability in response to soy protein.

Discussion

These findings regarding the effects of diet on gut permeability and the microbiome have important implications for experimental design. Single-source diets are ubiquitously used to maintain laboratory animals for medical research and feed details are frequently not reported in publications. Diet/phenotype interactions could have a large impact on inter-laboratory replicability in premedical research. For infants with fragile X, early-life diet could impact the severity of disease outcomes.

Gut microbiota modulation and inflammation mitigation in a murine model through a hull-less and purple grain barley genotype

Barley, increasingly recognized for its health benefits, contains bioactive compounds like beta-glucans and (poly)phenols. Newly developed purple barley varieties, enriched with anthocyanins, offer potential gut health benefits. This study examined the effects of a hull-less, purple-grain barley genotype, consumed as whole-grain or isolated fractions (bran and endosperm), on gut microbiota and inflammation in a murine model. Fifty male and female BALB/cB&J mice were assigned to five diets over six weeks: standard diet (SD), rice diet (RD), whole-grain barley (WGB), anthocyanin-rich barley bran (BB), and beta-glucan-rich endosperm (PG). The BB diet triggered anti-inflammatory signals as it reduced IFN-γ and IL-4 in females, lowered TNF-α in both sexes, and decreased C-Reactive Protein (CRP) in males compared to SD. The PG diet improved gut barrier integrity by lowering LPS-binding protein levels. Barley-based diets enhanced gut microbiota diversity, particularly, by increasing beneficial bacteria like Lactobacillus, Lachnospiraceae UCG-001, and Akkermansia. Notably, BB and PG elicited stronger effects than WGB, suggesting that grain fractionation modifies the food matrix, potentially enhancing the bioaccessibility and bioavailability of key bioactive compounds. These results underscore the benefits of purple barley-derived fractions in promoting gut health and reducing inflammation, supporting their potential role to protect against inflammation-related conditions.

Single-Cell Analysis Reveals Tissue-Specific T Cell Adaptation and Clonal Distribution Across the Human Gut-Liver-Blood Axis

Understanding T cell clonal relationships and tissue-specific adaptations is crucial for deciphering human immune responses, particularly within the gut-liver axis. We performed paired single-cell RNA and T cell receptor sequencing on matched colon (epithelium, lamina propria), liver, and blood T cells from the same human donors. This approach tracked clones across sites and assessed microenvironmental impacts on T cell phenotype. While some clones were shared between blood and tissues, colonic intraepithelial lymphocytes (IELs) exhibited limited overlap with lamina propria T cells, suggesting a largely resident population. Furthermore, tissue-resident memory T cells (TRM) in the colon and liver displayed distinct transcriptional profiles. Notably, our analysis suggested that factors enriched in the liver microenvironment may influence the phenotype of colon lamina propria TRM. This integrated single-cell analysis maps T cell clonal distribution and adaptation across the gut-liver-blood axis, highlighting a potential liver role in shaping colonic immunity.

Multi-Omics Analysis Reveals the Negative Effects of High-Concentrate Diets on the Colonic Epithelium of Dumont Lambs

Feeding HC diets has been found to induce metabolic dysregulation in the colon. However, the mechanisms by which changes in colonic flora and metabolites damage the colonic epithelium are poorly studied. Therefore, the present experiment used a multi-omics technique to investigate the mechanism of colonic injury induced by high-concentrate diets in lambs. Twelve male Dumont lambs were randomly split into two groups: a low-concentrate diet (LC = concentrate/forage = 30:70) group and a high-concentrate diet (HC = concentrate/forage = 70:30) group. The results showed that the HC group presented significantly increased lipopolysaccharide (LPS) concentrations in the colonic epithelium and significantly decreased serum total cholesterol (TC), superoxide dismutase (SOD), and glutathione peroxidase (GSH-Px) levels (p < 0.05), which led to cavities and inflammatory cell infiltration in the colonic epithelium. The HC group had significantly lower pH and less VFAs in colon contents, as well as a significantly increased abundance of bacteria of the genera [Eubacterium]_coprostanoligenes_group, Rikenellaceae_RC9_gut_group, Treponema, Clostridia_UCG-014, Alistipes, Ruminococcus, Christensenellaceae_R-7_group, UCG-002, Bacteroidales_RF16_group and Lachnospiraceae_AC2044_group compared to the LC diet group. These microorganisms significantly increased the level of metabolites of cholic acid, chenodeoxycholic acid, LysoPA (P-16:0/0:0), methapyrilene, and fusaric acid. A transcriptome analysis showed that cytokine-cytokine receptor interaction, glutathione metabolism, and the peroxisome signaling pathway were downregulated in the colon epithelium of the lambs fed the HC diet. Therefore, the HC diet caused epithelial inflammation and oxidative damage by affecting the interaction between the microbial flora of the colon and metabolites and the host epithelium, which eventually disrupted colon homeostasis and had a negative impact on sheep health.

Seleno-chitooligosaccharide-induced modulation of intestinal barrier function: Role of inflammatory cytokines, tight junction proteins, and gut microbiota in mice

This study aimed to explore the function of Seleno-chitooligosaccharide (SOA) on the intestinal barrier through regulation of inflammatory cytokines, tight junction protein, and gut microbiota in mice. The results of ELISA assay demonstrated that SOA significantly increased the levels of IL-2, IL-10, and IFN-γ in serum and ileum. Meanwhile, SOA increased the levels of IL-4 in the ileum (p < 0.05). In addition, Diamine Oxidase (DAO) concentration was decreased in ileum by SOA treatments (p < 0.05). The administration of SOA significantly upregulated the expression of ZO-1 and Occludin in the ileum (p < 0.05). By 16S rDNA sequencing, reduced ratio of Bacillota/Bacteroidota was observed in SOA treated mice. Within the phylum of Bacteroidota, SOA increased the relative abundance of Deferribacterota, uncultured Bacteroidales bacterium, and Bacteroides. Within the phylum of Bacillota, increased relative abundance of Erysipelatoclostridium and Lachnoclostridium, and reduced relative abundance of Ruminococcaceae UCG-010 were observed with SOA supplement. In summary, SOA has the potential to modulate the function of intestinal barrier function and prevent intestinal diseases.

Culturable Human Microorganisms and the Impact of Transportation Conditions on Cultivability

The composition of the human microbiome is a critical health indicator, and culture-independent methodologies have substantially advanced our understanding of human-associated microorganisms. However, precise identification and characterization of microbial strains require culture-based techniques. Recently, the resurgence of culturomics, combined with high-throughput sequencing technology, has reduced the high labor demand of pure culture methods, facilitating a more efficient and comprehensive acquisition of culturable microbial strains. This study employed an integrated approach combining culturomic and high-throughput sequencing to identify culturable microorganisms on the human scalp and in human saliva and feces. Several Staphylococcus strains were identified from the scalp, whereas anaerobic microorganisms were dominant in the saliva and fecal samples. Additionally, the study highlighted the beneficial effects of transportation conditions (liquid nitrogen treatment, dry ice transport, and dimethyl sulfoxide [DMSO] buffer) in preserving culturable microorganisms. A robust methodology was developed for the large-scale acquisition of culturable microorganisms with optimized transport conditions that enhance the potential for isolating a greater diversity of culturable strains.

Anthropogenic reverberations on the gut microbiome of dwarf chameleons (Bradypodion)

Exploration of the microbiome has been referred to as a final frontier in biological research. This is due to its precedence for generating insights on the holistic functioning of organismal biology by exploring the interactions between hosts and their associated symbiotic organisms. The microbiomes of many vertebrate groups still require exploration to advance current knowledge and fill previous knowledge gaps. This study generated initial descriptions of the bacterial microbiomes of three species of dwarf chameleon (Bradypodion) from the 16S rRNA gene region targeting the V3 and V4 hypervariable regions. This led to the successful identification of 1,073 and 4,502 independent amplicon sequence variants from buccal swab and faecal material samples, respectively. This newly acquired information is intended as a baseline for future work incorporating holobiont information. The diversity of microbial taxa suggests that the total dwarf chameleon microbiome is similar to other squamates investigated to date, as well as chelonians (Testudines). Microbial frequency differences were noted in comparison to crocodilians (Archosauria) and mammalian groups. Furthermore, this study aimed to examine the influence of habitat transformation on the composition of the microbiome in dwarf chameleons as each of the study species occupy both urban and natural habitats. Given that most urban habitats are highly transformed, the expectation was that microbial assemblages of the gastro-intestinal tracts of all three Bradypodion species would show significant differences between populations (i.e., natural, or urban). It was found, however, that the level of effect was contingent on species: B. melanocephalum populations showed noticeable microbiome differences between urban and natural populations; B. thamnobates showed variations in microbial community dispersions between populations; and B. setaroi showed no significant microbiome differences based on diversity metrics although some frequency differences, in microbiome composition, were observed between populations. We suggest that the magnitude of difference between the habitats occupied by the populations is a factor, given the apparent disparity between the natural and urban habitats for B. melanocephalum as compared to the other two species.

Bioprospecting of 101 facultative rumen bacterial isolates through comprehensive genome analysis

BACKGROUND

Microbes within the rumen play a pivotal role in the digestion of feed ingested by the ruminants. Researchers have been investigating microbes within rumen to assess its genetic capabilities, which hold immense potential across various fields including agro-industrial advantages. Since rumen is preliminary an anaerobic sac, numerous anaerobic bacteria and fungi have been isolated and characterized, however facultative anaerobic bacteria yet not fully investigated.

METHODS AND RESULTS

In present study, we isolated, characterized and performed whole genome analysis of 101 facultative anaerobic bacteria from rumen, offering a unique perspective compared to metagenomic approaches. All assembled genomes were of high quality, i.e. completeness 100% (only seven were between 92 and 99.5%) and only two had contamination > 5%. We identified 9,542 sequences of Carbohydrate-Active Enzymes (CAZymes). Over 8,136 of these CAZymes were full-length sequences, with 2,048 harbouring signal peptides also. Xylan (n = 634), pectin (n = 604), and starch (n = 312) degrading enzyme sequences were dominant. Several isolates also harbour secondary metabolite biosynthesis gene clusters for various metabolites, including fengycin, lichenysin, bacillibactins, bacilysin etc. All the isolates have metabolic versatility, encompassing pathways such as carbohydrate, amino acid, lipid, and vitamin and cofactor metabolism. Intriguingly, lipoic acid metabolism was absent in most of these facultative bacterial isolates.

CONCLUSION

This comprehensive study sheds light on the genetic potential of culturable facultative rumen bacteria, emphasizing their pivotal roles in carbohydrate degradation, secondary metabolite production, and metabolic diversity. These findings hold promise for enhancing ruminant nutrition, advancing eco-friendly biomass conversion, and bolstering bioprospecting of industrially important biocules and enzymes biofuel production.

Changes in the intestinal microbiota induced by the postnatal environment and their association with hypertension

It has been established that cross-fostering impacts the development of hypertension in spontaneously hypertensive rats (SHR). However, the ability of the cross-fostering protocol to shape gut microbiota profile in SHR and impact hypertension is not known. In this sense, the current study explored the influence of normotensive and hypertensive postnatal environments on the intestinal microbiota structure, composition, and functional capacity of SHR and Wistar rats. Our findings revealed significant differences in the microbiota's composition and its metabolic activity in young non-fostered SHR (SS) vs. Wistar (WW) rats, even before hypertension onset, characterized by a reduction of the "low-abundance" bacterial genera, a diminished availability of fecal butyrate and elevated hydrogen sulfide (H2S) production by the SS gut microbiota. Despite influencing the microbiota of both strains, cross-fostering did not fully replicate the microbiota composition of the naturally reared groups in the SHR nursed by Wistar mothers (SW), or in the Wistar rats breastfed by SHR mothers (WS). The SW group had fewer significant genera identified at the Partial Least Squares Discriminant Analysis (PLS-DA), despite resembling the genera profile identified in the normotensive group. While sharing bacterial genera with both SS and WW groups, the WS group is distinguished by its unique microbial composition, particularly by a greater diversity of the 'low-abundance' bacterial genera. Moreover, decreased systolic blood pressure was observed in the SW group compared to the SS group in adulthood. Thus, we could establish a link between microbiota composition and hypertension development, associating it with the loss of the "low-abundance" bacterial taxa. Our data suggest that the postnatal environment is pivotal to promoting gut microbiota compositional changes and contributes to hypertension development.

Gut microbiota in symptomatic uncomplicated diverticular disease stratifies by severity of abdominal pain

OBJECTIVE

Patients with symptomatic uncomplicated diverticular disease (SUDD) may have a disrupted gut microbiota. However, current data are from small sample studies, and reported associations vary widely across studies. We aimed to profile the fecal microbiota in SUDD patients enrolled in primary care.

METHODS

A retrospective study was conducted in SUDD ( N  = 72) and asymptomatic diverticulosis (AD) ( N  = 30), the latter serving as a control group.

RESULTS

No significant differences in alpha and beta diversity were found between SUDD and AD, but SUDD was discriminated by a higher relative abundance of the family Streptococcaceae and the genera Alistipes , Agathobacter , and Butyricimonas . Interestingly, the gut microbiota of SUDD patients stratified by the severity of abdominal pain [according to the visual analog scale (VAS)]. In particular, higher diversity and health-associated taxa (such as Bifidobacterium , Eubacterium coprostanoligenes group, and Dorea ) characterized mild (VAS score 1-3) SUDD, Proteobacteria , Veillonellaceae and Blautia moderate (VAS score 4-7) SUDD, and Prevotellaceae and Megasphaera severe (VAS score 8-10) SUDD.

CONCLUSION

Our analysis suggests that specific taxa may be related to SUDD, but the associations vary depending on the severity of abdominal pain. In addition to advancing our ecological understanding of this complex disease, our findings may pave the way for the incorporation of gut microbiota profiling into clinical practice to aid patient management, including stratification and treatment.

Use of a Novel Passive E-Nose to Monitor Fermentable Prebiotic Fiber Consumption

We developed a home-based electronic nose (E-Nose) to passively monitor volatile organic compounds (VOCs) emitted following bowel movements and assessed its validity by correlating the output with prebiotic fiber intake. Healthy, non-overweight participants followed a three-week protocol which included the following: (1) installing the E-Nose in their bathroom; (2) activating the device following each bowel movement; (3) recording their dietary intake; (4) consuming a fiber bar (RiteCarbs) containing a blend of 10 g of prebiotic fiber daily during weeks two and three; and (5) submit stool specimens at the beginning and end of the study for 16S rRNA gene sequencing and analysis. Participants' fecal microbiome displayed significantly increased relative abundance of putative total SCFA-producing genera (p = 0.0323) [total acetate-producing genera (p = 0.0214), total butyrate-producing genera (p = 0.0131)] and decreased Gram-negative proinflammatory genera (p = 0.0468). Prebiotic intervention significantly increased the participants' fiber intake (p = 0.0152), E-Nose Min/Max (p = 0.0339), and area over the curve in VOC-to-fiber output (p = 0.0044). Increased fiber intake was negatively associated (R2 = 0.53, p = 0.026) with decreased relative abundance of putative Gram-negative proinflammatory genera. This proof-of-concept study demonstrates that a prototype E-Nose can noninvasively detect a direct connection between fiber intake and VOC outputs in a home-based environment.

Machine learning models reveal microbial signatures in healthy human tissues, challenging the sterility of human organs

Background

The presence of microbes within healthy human internal organs still remains under question. Our study endeavors to discern microbial signatures within normal human internal tissues using data from the Genotype-Tissue Expression (GTEx) consortium. Machine learning (ML) models were developed to classify each tissue type based solely on microbial profiles, with the identification of tissue-specific microbial signatures suggesting the presence of distinct microbial communities inside tissues.

Methods

We analyzed 13,871 normal RNA-seq samples from 28 tissues obtained from the GTEx consortium. Unaligned sequencing reads with the human genome were processed using AGAMEMNON, an algorithm for metagenomic microbial quantification, with a reference database comprising bacterial, archaeal, and viral genomes, alongside fungal transcriptomes. Gradient-boosting ML models were trained to classify each tissue against all others based on its microbial profile. To validate the findings, we analyzed 38 healthy living tissue samples (samples from healthy tissues obtained from living individuals, not deceased) from an independent study, as the GTEx samples were derived from post-mortem biopsies.

Results

Tissue-specific microbial signatures were identified in 11 out of the 28 tissues while the signatures for 8 tissues (Muscle, Heart, Stomach, Colon tissue, Testis, Blood, Liver, and Bladder tissue) demonstrated resilience to in silico contamination. The models for Heart, Colon tissue, and Liver displayed high discriminatory performance also in the living dataset, suggesting the presence of a tissue-specific microbiome for these tissues even in a living state. Notably, the most crucial features were the fungus Sporisorium graminicola for the heart, the gram-positive bacterium Flavonifractor plautii for the colon tissue, and the gram-negative bacterium Bartonella machadoae for the liver.

Conclusion

The presence of tissue-specific microbial signatures in certain tissues suggests that these organs are not devoid of microorganisms even in healthy conditions and probably they harbor low-biomass microbial communities unique to each tissue. The discoveries presented here confront the enduring dogma positing the sterility of internal tissues, yet further validation through controlled laboratory experiments is imperative to substantiate this hypothesis. Exploring the microbiome of internal tissues holds promise for elucidating the pathophysiology underlying both health and a spectrum of diseases, including sepsis, inflammation, and cancer.

Chronic inflammation in post-acute sequelae of COVID-19 modulates gut microbiome: a review of literature on COVID-19 sequelae and gut dysbiosis

BACKGROUND

Long COVID or Post-acute sequelae of COVID-19 is an emerging syndrome, recognized in COVID-19 patients who suffer from mild to severe illness and do not recover completely. Most studies define Long COVID, through symptoms like fatigue, brain fog, joint pain, and headache prevailing four or more weeks post-initial infection. Global variations in Long COVID presentation and symptoms make it challenging to standardize features of Long COVID. Long COVID appears to be accompanied by an auto-immune multi-faceted syndrome where the virus or viral antigen persistence causes continuous stimulation of the immune response, resulting in multi-organ immune dysregulation.

MAIN TEXT

This review is focused on understanding the risk factors of Long COVID with a special emphasis on the dysregulation of the gut-brain axis. Two proposed mechanisms are discussed here. The first mechanism is related to the dysfunction of angiotensin-converting enzyme 2 receptor due to Severe Acute Respiratory Syndrome Corona Virus 2 infection, leading to impaired mTOR pathway activation, reduced AMP secretion, and causing dysbiotic changes in the gut. Secondly, gut-brain axis dysregulation accompanied by decreased production of short-chain fatty acids, impaired enteroendocrine cell function, and increased leakiness of the gut, which favors translocation of pathogens or lipopolysaccharide in circulation causing the release of pro-inflammatory cytokines. The altered Hypothalamic-Pituitary-Adrenal axis is accompanied by the reduced level of neurotransmitter, and decreased stimulation of the vagus nerve, which may cause neuroinflammation and dysregulation of serum cortisol levels. The dysbiotic microbiome in Long COVID patients is characterized by a decrease in beneficial short chain fatty acid-producing bacteria (Faecalibacterium, Ruminococcus, Dorea, and Bifidobacterium) and an increase in opportunistic bacteria (Corynebacterium, Streptococcus, Enterococcus). This dysbiosis is transient and may be impacted by interventions including probiotics, and dietary supplements.

CONCLUSIONS

Further studies are required to understand the geographic variation, racial and ethnic differences in phenotypes of Long COVID, the influence of viral strains on existing and emerging phenotypes, to explore long-term effects of gut dysbiosis, and gut-brain axis dysregulation, as well as the potential role of diet and probiotics in alleviating those symptoms.

High leafy and root vegetables and high rice dietary patterns were associated with primary and secondary bile acid levels in the feces

Colorectal cancer has the second highest mortality among cancer sites worldwide, with increasing morbidity, high recurrence rates, and even poorer postoperative quality of life. Therefore, preventive strategies for colorectal cancer should be established. This study aimed to cross-sectionally explore dietary patterns affecting the intestinal metabolism of bile acids (BAs), a risk factor for colorectal cancer, in young Japanese women. We collected fecal samples for intestinal microbiota and BA analysis. We used the Bristol scale to determine 1-week defecation status. Moreover, the brief-type self-administered diet history questionnaire was used for habitual dietary intake status. Reduced-rank regression analysis revealed dietary patterns related to fecal BA levels. The relationship between dietary patterns and fecal BA levels was adjusted for defecation status and intestinal microbiota variables using analysis of covariance. Reduced-rank regression analysis generated two dietary pattern scores related to fecal BA levels. First, the score was associated with a greater intake of leafy and root vegetables, and higher values were associated with greater fecal cholic and chenodeoxycholic acid levels and lower deoxycholic and lithocholic acid levels. Second, the score was associated with greater rice intake and lower Western sweets, pork, beef, and egg intake, and higher values were associated with lower deoxycholic and lithocholic acid levels. These relationships remained after adjusting for intestinal microbiota and defecation status variables.

Metagenome-guided culturomics for the targeted enrichment of gut microbes

The gut microbiome significantly impacts human health, yet cultivation challenges hinder its exploration. Here, we combine deep whole-metagenome sequencing with culturomics to selectively enrich for taxa and functional capabilities of interest. Using a modified commercial base medium, 50 growth modifications were evaluated, spanning antibiotics, physico-chemical conditions, and bioactive compounds. Whole-metagenome sequencing identified medium additives, like caffeine, that enhance taxa often associated with healthier subjects (e.g., Lachnospiraceae, Oscillospiraceae, Ruminococcaceae). We also explore the impact of modifications on the composition of cultured communities and establish a link between medium preference and microbial phylogeny. Leveraging these insights, we demonstrate that combinations of media modifications can further enhance the targeted enrichment of taxa and metabolic functions, such as Collinsella aerofaciens, or strains harboring biochemical pathways involved in dopamine metabolism. This streamlined, scalable approach unlocks the potential for selective enrichment, advancing microbiome research by understanding the impact of different cultivation parameters on gut microbes.

Characteristics of gut microbiota profiles in Asian elephants (Elephas maximus) with gastrointestinal disorders

Colic and diarrhea are common gastrointestinal (GI) disorders in captive Asian elephants, which can severely impact health and lead to mortality. Gut dysbiosis, indicated by alterations in gut microbiome composition, can be observed in individuals with GI disorders. However, changes in gut microbial profiles of elephants with GI disorders have never been investigated. Thus, this study aimed to elucidate the profiles of gut microbiota in captive elephants with different GI symptoms. Fecal samples were collected from eighteen elephants in Chiang Mai, Thailand, including seven healthy individuals, seven with impaction colic, and four with diarrhea. The samples were subjected to DNA extraction and amplification targeting the V3-V4 region of 16S rRNA gene for next-generation sequencing analysis. Elephants with GI symptoms exhibited a decreased microbial stability, as characterized by a significant reduction in microbiota diversity within individual guts and notable differences in microbial community composition when compared with healthy elephants. These changes included a decrease in the relative abundance of specific bacterial taxa, in elephants with GI symptoms such as a reduction in genera Rubrobacter, Rokubacteria, UBA1819, Nitrospira, and MND1. Conversely, an increase in genera Lysinibacillus, Bacteroidetes_BD2-2, and the family Marinifilaceae was observed when, compared with the healthy group. Variations in taxa of gut microbiota among elephants with GI disorders indicated diverse microbial characteristics associated with different GI symptoms. This study suggests that exploring gut microbiota dynamics in elephant health and GI disorders can lead to a better understanding of food and water management for maintaining a healthy gut and ensuring the longevity of the elephants.

Prebiotics as an adjunct therapy for posttraumatic stress disorder: a pilot randomized controlled trial

Introduction

Posttraumatic stress disorder (PTSD) is a debilitating disorder characterized by intrusive memories, avoidance, negative thoughts and moods, and heightened arousal. Many patients also report gastrointestinal symptoms. Cognitive behavioral therapy (CBT) is an evidence-based treatment approach for PTSD that successfully reduces symptoms. However, many patients still meet criteria for PTSD after treatment or continue to have symptoms indicating the need for new treatment strategies for PTSD. Patients with PTSD have a disrupted intestinal microbiome (i.e., dysbiosis) which can promote neuroinflammation; thus, modulation of the microbiome could be an alternative or adjunct treatment approach for PTSD.

Methods

The current study was a 12-week, double-blind, placebo-controlled trial seeking to understand if CBT combined with a microbiota-modifying, prebiotic fiber intervention would beneficially impact clinical outcomes in veterans with PTSD (n = 70). This proof-of-concept, pilot trial was designed to assess: (1) the relationship between severity of PTSD symptoms and microbiota composition and SCFA levels (i.e., acetate, propionate, butyrate), (2) if CBT treatment with a concomitant prebiotic fiber intervention would beneficially impact clinical outcomes in veterans with PTSD, (3) evaluate the feasibility and acceptability of a prebiotic intervention as an adjunct treatment to CBT, and (4) assess the impact of treatment on the intestinal microbiota and stool SCFA (i.e., mechanism).

Results

This study found that PTSD severity may be associated with reduced abundance of taxa capable of producing the SCFA propionate, and that a subset of individuals with PTSD may benefit from a microbiota-modifying prebiotic intervention.

Conclusion

This study suggests that targeting the intestinal microbiome through prebiotic supplementation could represent a promising avenue for enhancing treatment outcomes in some individuals with PTSD.

Clinical trial registration

https://clinicaltrials.gov/, identifier NCT05424146.

Gingerols: Preparation, encapsulation, and bioactivities focusing gut microbiome modulation and attenuation of disease symptoms

BACKGROUND

Gut dysbiosis, chronic diseases, and microbial recurrent infections concerns have driven the researchers to explore phytochemicals from medicinal and food homologous plants to modulate gut microbiota, mitigate diseases, and inhibit pathogens. Gingerols have attracted attention as therapeutic agents due to their diverse biological activities like gut microbiome regulation, gastro-protective, anti-inflammatory, anti-microbial, and anti-oxidative effects.

PURPOSE

This review aimed to summarize the gingerols health-promoting potential, specifically focusing on the regulation of gut microbiome, attenuation of disease symptoms, mechanisms of action, and signaling pathways involved.

METHOD

Research findings from experimental and clinical studies have been summarized regarding gingerols effects on the modulation of gut microbiome and its metabolites, and attenuation of disease symptoms.

RESULTS

Gingerols are phenolic compounds characterized by a common 3-methoxy-4-hydroxyphenyl moiety in their chemical structures, and further divided into different gingerol types, including gingerols (major), shogaols, paradols, gingerdiols, gingerdiones, and zingerones (minor). Advanced extraction techniques (e.g., ionic liquid-based-, enzyme-assisted-, microwave-assisted-, pressurized liquid-, ultrasound-assisted-, and supercritical fluid extractions) were reported as optimal alternatives to conventional methods for gingerols extraction. Research studies reported that gingerols positively modulated the composition of gut microbiome that helped to combat disease symptoms (e.g., obesity by decreasing weight gain- (Lactobacillus reuteri and Lachnospiraceae) and increasing weight loss associated-bacteria (Akkermansia, Muribaculaceae, and Alloprevotella). Gingerols intervention also ameliorated ulcerative colitis by increasing relative abundance of the beneficial bacteria (Akkermansia, Lachnospiraceae NK4A136, and Muribaculaceae_norank), and decreasing pathogenic microorganisms (Bacteroides, Parabacteroides, and Desulfovibrio). Emerging delivery systems (e.g., microcapsules, nanoparticles, nanostructured lipid carriers, nanoemulsions, and nanoliposomes) can enhance the bioavailability and therapeutic efficacy of gingerols by preserving their inherent properties and addressing challenges of stability, solubility, and absorption.

CONCLUSION

Gingerols are promising therapeutic agents to modulate gut microbiome (increase beneficial bacteria and inhibit pathogenic microbes), and attenuate chronic disease symptoms such as diabetes, colitis, obesity, oxidative stress, and cancer. Despite significant progress, challenges persist in transforming research findings into industrial applications, such as stability and solubility during processing and low bioavailability in the distal gut to impart desirable health benefits.

Oral bacteriophage therapy effectively prevent and control of Clostridium perfringens type c infections in newborn piglets

Clostridium perfringens (C. perfringens) type C exhibits strong pathogenicity, often leading to swine dysentery, severely affecting the economic efficiency of the pig farming industry. Bacteriophages as bacterial viruses have many natural advantages and are potent candidates for controlling bacterial infections. In this study, a lytic C. perfringens phage designed as vB_CpeP_15N3 was isolated with the host C. perfringens type C CVCC1155, and its potential for therapy was determined in vitro and in vivo. Despite the narrow host range, phage vB_CpeP_15N3 exhibited a large burst size of 102 PFU/cell following a short latent period of 10 min. In addition, phage vB_CpeP_15N3 remained stable at temperatures ranging from 4 to 50°C and pH levels from 5 to 9 and had a strong antibacterial effect in vitro. Through whole-genome analysis, phage vB_CpeP_15N3 belongs to the family Guelinviridae, genus Brucesealvirus with no genes related to lysogeny and bacterial virulence or resistance. We further demonstrated that phage vB_CpeP_15N3 by oral administration for preventive purposes could significantly alleviate clinical symptoms and jejunal lesions of newborn piglets through the reduced colonization of C. perfringens type C in the jejunum and the level of CPB toxin in the content of jejunum in the newborn piglet model of CVCC1155 infection. In addition, phage vB_CpeP_15N3 by oral administration for preventive purposes could improve the diversity and abundance of the jejunum microbiota in newborn piglets. Moreover, the prevention by phage vB_CpeP_15N3 obtained more effective therapeutic results than phage and gentamicin treatments. Taken together, these findings suggested that phage vB_CpeP_15N3 is a promising alternative of antibiotics for preventing and controlling C. perfringens type C infection of newborn piglets.

Associations between dietary fibers and gut microbiome composition in the EDIA longitudinal infant cohort

BACKGROUND

The infant gut microbiome undergoes rapid changes in the first year of life, supporting normal development and long-term health. Although diet shapes this process, the role of fibers in complementary foods on gut microbiome maturation is poorly understood.

OBJECTIVES

We explored how the transition from human milk to fibers in complementary foods shapes the taxonomic and functional maturation of the gut microbiome within the first year of life.

METHODS

We assessed the longitudinal and cross-sectional development of infant gut microbiomes (N = 68 infants) and metabolomes (N = 33 infants) using linear mixed models to uncover their associations to dietary fibers and their food sources. Fiber intakes were assessed with 3-d food records (months 3, 6, 9, and 12) relying on CODEX-compliant fiber fraction values, and questionnaires tracked the overall complementary food introduction. Bacterial species were identified and quantified via MetaPhlAn2 from metagenomic data, and metabolomic profiles were obtained using 4 LC-MS methods.

RESULTS

We identified 176 complementary food fiber-bacterial species associations. First plant-based fibers associated with microbiota compositions similar to breastfeeding, and further associated with aromatic amino acid-derived metabolites, including 5-hydroxyindoleacetic acid (total dietary fiber - complementary foods (g) - β = 3.50, CI: 2.48, 4.52, P = 6.53 × 10-5). Distinct fibers from different food categories showed unique associations with specific bacterial taxa. Key species, such as Faecalibacterium prausnitznii, associated with oat fibers (g/MJ, β = 2.18, confidence interval: 1.36, 2.84, P = 6.12 × 10-6), reflective of maturing microbial communities. Fiber intake during weaning associated with shifts in metabolite profiles, including immunomodulatory metabolites, with fiber effects observed in a source- and timing-dependent manner, implicated in gradual microbiome diversification.

CONCLUSIONS

Introducing complementary dietary fibers during the weaning period supports gut microbiome diversification and stabilization. Even minor dietary variations shows significant associations with microbial taxa and functions from the onset of weaning, highlighting the importance of infant dietary recommendations that support the gut microbiome maturation during early life. This trial was registered at clinicaltrials.gov as registration number NCT01735123.

Bacterial Organelles in Iron Physiology

Bacteria were once thought to be simple organisms, lacking the membrane-bound organelles found in eukaryotic cells. However, recent advancements in microscopy have changed this view, revealing a diverse array of organelles within bacterial cells. These organelles, surrounded by lipid bilayers, protein-lipid monolayers, or proteinaceous shells, play crucial roles in facilitating biochemical reactions and protecting cells from harmful byproducts. Unlike eukaryotic organelles, which are universally present, bacterial organelles are species-specific and induced only under certain conditions. This review focuses on the bacterial organelles that contain iron, an essential micronutrient for all life forms but potentially toxic when present in excess. To date, three types of iron-related bacterial organelles have been identified: two membrane-bound organelles, magnetosomes and ferrosomes, and one protein-enclosed organelle, the encapsulated ferritin-like proteins. This article provides an updated overview of the genetics, biogenesis, and physiological functions of these organelles. Furthermore, we discuss how bacteria utilize these specialized structures to adapt, grow, and survive under various environmental conditions.

Exploring the relationship between Faecalibacterium duncaniae and Escherichia coli in inflammatory bowel disease (IBD): Insights and implications

Inflammatory bowel disease (IBD) is a group of disorders characterized by an inflammation of the gastrointestinal tract (GIT) and represents a major social and economic burden. Despite ongoing research into the etiology and pathophysiology of this multifactorial disease, treatment options remain limited. From this perspective, the gut microbiota has emerged as a potential player in the pathogenesis of IBD, and animal and human studies support this hypothesis. Indeed, the human gut is one of the most complex ecological communities (composed of 1013-1014 microorganisms) that plays a critical role in human health by influencing normal physiology and disease susceptibility through its collective metabolic activities and host interactions. In addition, live probiotic bacteria present in some food products (which transit through the GIT) have been shown to interact with the host immune system and confer several health benefits. The aim of this review is to provide an overview of the link between Faecalibacterium duncaniae and Escherichia coli and IBD, highlighting the main areas of research in this field. An ecological perspective on the gut microbiota may offer new insights for the development of clinical therapies targeting this bacterial community to improve human health.

Microbial diversity and biosafety judgment of digestates derived from different biogas plants for agricultural applications

The composition of microbial communities is the key to effective anaerobic digestion (AD). The microbiome driving the AD process has been extensively researched, whereas the influence of specific substrates on the microbiome of digestate remains insufficiently investigated. Digestate has considerable potential for use in soil fertilization and bioremediation, therefore its biological safety should be monitored. Moreover, the knowledge about the composition of microbial communities and their interconnections in digestate should be extended, due to the impact on soil microbiota and its functionality. The aim of this study was a comprehensive assessment of the (1) sanitary quality, (2) core microbiome, and (3) microbial interactions in digestates collected from three full-scale agricultural biogas plants, with particular emphasis on their applicability from the perspective of the resident microbiota. Analyzed samples of digestate were derived from various substrates used for AD, including plant- and animal-based materials, and industrial waste. The study demonstrated that the phyla Bacillota, Bacteroidota, and Cloacimonadota were the most dominant in digestates regardless of the composition of the processed substrates, however, member composition at the genus level differed significantly between samples. In addition, we observed that microbial genera belonging to the less prevalent phyla play an integral role in the forming of microbial community interactions. Dominant microbial taxa with broad metabolic capabilities, potentially improving soil quality and functionality, have been identified. Moreover, we confirmed, that digestate samples were free of analyzed pathogenic bacteria and parasites. The study results indicate that digestate may have an immense fertilizing and bioremediation potential that has not been fully availed of to date.

Human microbiome in post-acute COVID-19 syndrome (PACS)

The global COVID-19 pandemic, which began in 2019, is still ongoing. SARS-CoV-2, also known as the severe acute respiratory syndrome coronavirus 2, is the causative agent. Diarrhea, nausea, and vomiting are common GI symptoms observed in a significant number of COVID-19 patients. Additionally, the respiratory and GI tracts express high level of transmembrane protease serine 2 (TMPRSS2) and angiotensin-converting enzyme-2 (ACE2), making them primary sites for human microbiota and targets for SARS-CoV-2 infection. A growing body of research indicates that individuals with COVID-19 and post-acute COVID-19 syndrome (PACS) exhibit considerable alterations in their microbiome. In various human disorders, including diabetes, obesity, cancer, ulcerative colitis, Crohn's disease, and several viral infections, the microbiota play a significant immunomodulatory role. In this review, we investigate the potential therapeutic implications of the interactions between host microbiota and COVID-19. Microbiota-derived metabolites and components serve as primary mediators of microbiota-host interactions, influencing host immunity. We discuss the various mechanisms through which these metabolites or components produced by the microbiota impact the host's immune response to SARS-CoV-2 infection. Additionally, we address confounding factors in microbiome studies. Finally, we examine and discuss about a range of potential microbiota-based prophylactic measures and treatments for COVID-19 and PACS, as well as their effects on clinical outcomes and disease severity.

Diversity of bacteria within the human gut and its contribution to the functional unity of holobionts

The composition of bacteria in the human colon has been a subject of interest since the beginning of microbiology. With the development of methods for culturing strict anaerobic bacteria under multiple culture conditions, it was shown the gut contained more than 400 bacterial species and different people harbor different abundant species. The term "gut microbiome" in this review refers to bacteria studied in stool samples. Molecular methods for determining the bacterial composition of human gut has revealed more than 3000 species and less than 130 genera, indicating that the diversity of human colonic bacteria is concentrated at the species and strain levels. This review concludes with a discussion of how diversity can lead to unity of individual holobionts, between holobionts, and between populations. One of the reasons for the unity is that different bacterial species can have similar functional genes.

Sugar Composition of Thai Desserts and Their Impact on the Gut Microbiome in Healthy Volunteers: A Randomized Controlled Trial

BACKGROUND

The relationship between consuming Thai desserts-predominantly composed of carbohydrates-and gut microbiome profiles remains unclear. This study aimed to evaluate the effects of consuming various Thai desserts with different GI values on the gut microbiomes of healthy volunteers.

METHODS

This open-label, parallel randomized clinical trial involved 30 healthy individuals aged 18 to 45 years. Participants were randomly assigned to one of three groups: Phetchaburi's Custard Cake (192 g, low-GI group, n = 10), Saraburi's Curry Puff (98 g, medium-GI group, n = 10), and Lampang's Crispy Rice Cracker (68 g, high-GI group, n = 10), each consumed alongside their standard breakfast. Fecal samples were collected at baseline and 24 h post-intervention for metagenomic analysis of gut microbiome profiles using 16S rRNA gene sequencing.

RESULTS

After 24 h, distinct trends in the relative abundance of various gut microbiota were observed among the dessert groups. In the high-GI dessert group, the abundance of Collinsella and Bifidobacterium decreased compared to the low- and medium-GI groups, while Roseburia and Ruminococcus showed slight increases. Correlation analysis revealed a significant negative relationship between sugar intake and Lactobacillus abundance in the medium- and high-GI groups, but not in the low-GI group. Additionally, a moderately negative association was observed between Akkermansia abundance and sugar intake in the high-GI group. These bacteria are implicated in energy metabolism and insulin regulation. LEfSe analysis identified Porphyromonadaceae and Porphyromonas as core microbiota in the low-GI group, whereas Klebsiella was enriched in the high-GI group, with no predominant bacteria identified in the medium-GI group.

CONCLUSIONS

The findings suggest that Thai desserts with varying GI levels can influence specific gut bacteria, though these effects may be temporary.

Zuogui Jiangtang Jieyu prescription improves diabetes-related depression by modulation of gut microbiota and neuroinflammation in hippocampus

Context

There is a significant challenge associated with the co-morbidity of mental and physical illnesses throughout the world. A classic example of mental/physical co-morbidity is diabetes-related depression (DD).

Objective

DD is treated with Zuogui Jiangtang Jieyu prescription (ZJJ). Diabetes and psychiatric disorders are associated with dysbiosis of the gut microbiota. In this study, the aim is to examine the effects of ZJJ on gut microbiota and neuroinflammation in DD.

Methods

A model of DD was established and treated with medium and high doses of ZJJ as well as Metformin & Fluoxetine. A detection of depressive-like behavior was then conducted on the rats. Proinflammatory cytokines were measured in cerebrospinal fluid, and HPA axis-related proteins, glucose metabolism, and lipopolysaccharide (LPS) were measured in serum. Fecal samples from each group were collected and analyzed by 16S rRNA sequencing; TLR4 and MyD88 levels were detected by Western blot and immunohistochemistry (IHC) in the hippocampus.

Results

High doses of ZJJ (ZJJ-H) were found to alleviate HPA axis hyperactivity and improve gut microbiota in rats with DD. Additionally, ZJJ treatment attenuated the inflammatory response in cerebrospinal fluid, e.g. a significant reduction in proinflammatory factors, a decrease in serum LPS levels, and an inhibition of TLR4/MyD88-related pathways in the hippocampus.

Discussion and conclusion

ZJJ improved DD glucose metabolism and alleviated depression-like behaviors by improving gut microbiota and inhibiting hippocampal TLR4/Myd88 signaling pathways.

The role of gut microbial β-glucuronidases in carcinogenesis and cancer treatment: a scoping review

INTRODUCTION

The human gut microbiota influence critical functions including the metabolism of nutrients, xenobiotics, and drugs. Gut microbial β-glucuronidases (GUS) enzymes facilitate the removal of glucuronic acid from various compounds, potentially affecting anti-cancer drug efficacy and reactivating carcinogens. This review aims to comprehensively analyze and summarize studies on the role of gut microbial GUS in cancer and its interaction with anti-cancer treatments. Its goal is to collate and present insights that are directly relevant to patient care and treatment strategies in oncology.

METHODS

This scoping review followed PRISMA-ScR guidelines and focused on primary research exploring the role of GUS within the gut microbiota related to cancer etiology and anti-cancer treatment. Comprehensive literature searches were conducted in PubMed, Embase, and Web of Science.

RESULTS

GUS activity was only investigated in colorectal cancer (CRC), revealing increased fecal GUS activity, variations in the gut microbial composition, and GUS-contributing bacterial taxa in CRC patients versus controls. Irinotecan affects gastrointestinal (GI) health by increasing GUS expression and shifting gut microbial composition, particularly by enhancing the presence of GUS-producing bacteria, correlating with irinotecan-induced GI toxicities. GUS inhibitors (GUSi) can mitigate irinotecan's adverse effects, protecting the intestinal barrier and reducing diarrhea.

CONCLUSION

To our knowledge, this is the first review to comprehensively analyze and summarize studies on the critical role of gut microbial GUS in cancer and anti-cancer treatment, particularly irinotecan. It underscores the potential of GUSi to reduce side effects and enhance treatment efficacy, highlighting the urgent need for further research to integrate GUS targeting into future anti-cancer treatment strategies.

Is there a role for intestinal sporobiota in the antimicrobial resistance crisis?

Antimicrobial resistance (AMR) is a complex issue requiring specific, multi-sectoral measures to slow its spread. When people are exposed to antimicrobial agents, it can cause resistant bacteria to increase. This means that the use, misuse, and excessive use of antimicrobial agents exert selective pressure on bacteria, which can lead to the development of "silent" reservoirs of antimicrobial resistance genes. These genes can later be mobilized into pathogenic bacteria and contribute to the spread of AMR. Many socioeconomic and environmental factors influence the transmission and dissemination of resistance genes, such as the quality of healthcare systems, water sanitation, hygiene infrastructure, and pollution. The sporobiota is an essential part of the gut microbiota that plays a role in maintaining gut homeostasis. However, because spores are highly transmissible and can spread easily, they can be a vector for AMR. The sporobiota resistome, particularly the mobile resistome, is important for tracking, managing, and limiting the spread of antimicrobial resistance genes among pathogenic and commensal bacterial species.

Structural characterization and immunomodulatory activity of polysaccharides from the lateral roots of Aconitum carmichaelii

Two polysaccharides, named FPS1-1 and FPS1-2, were separated from the neutral polysaccharides of the lateral roots of Aconitum carmichaelii, a widely used traditional Chinese medicine (Fuzi in Chinese). The monosaccharide composition analysis indicated that both FPS1-1 and FPS1-2 were glucans. However, further physicochemical analysis of FPS1-1 and FPS1-2 revealed distinct properties between the two glucans. FPS1-1 had a molecular weight (Mw) of 106.23 kDa with a spherical conformation, while FPS1-2 had a lower Mw of 19.23 kDa with a random coil conformation. The structure of FPS1-2 was further determined as a glucan whose backbone structure was composed of →4)-α-D-Glcp-(1→. The immunological activities of two polysaccharides were evaluated by a cyclophosphamide (CTX)-induced immunodeficiency model in mice. The result showed that FPS1-2 could restore CTX-induced immunosuppression by modulating CD4+ T cells differentiation and promoting cytokine secretion. Notably, FPS1-2 could modulate the colonic short-chain fatty acid (SCFA) levels and reverse the gut microbial dysbiosis induced by CTX. These findings reveal the potential benefits of Fuzi polysaccharides and provide evidences for developing immunologically functional products from Fuzi polysaccharides.

The dynamic crosslinking between gut microbiota and inflammation during aging: reviewing the nutritional and hormetic approaches against dysbiosis and inflammaging

The early-life gut microbiota (GM) is increasingly recognized for its contributions to human health and disease over time. Microbiota composition, influenced by factors like race, geography, lifestyle, and individual differences, is subject to change. The GM serves dual roles, defending against pathogens and shaping the host immune system. Disruptions in microbial composition can lead to immune dysregulation, impacting defense mechanisms. Additionally, GM aids digestion, releasing nutrients and influencing physiological systems like the liver, brain, and endocrine system through microbial metabolites. Dysbiosis disrupts intestinal homeostasis, contributing to age-related diseases. Recent studies are elucidating the bacterial species that characterize a healthy microbiota, defining what constitutes a 'healthy' colonic microbiota. The present review article focuses on the importance of microbiome composition for the development of homeostasis and the roles of GM during aging and the age-related diseases caused by the alteration in gut microbial communities. This article might also help the readers to find treatments targeting GM for the prevention of various diseases linked to it effectively.

Current Trends and Technological Advancements in the Use of Oxalate-Degrading Bacteria as Starters in Fermented Foods-A Review

Nephrolithiasis is a medical condition characterized by the existence or development of calculi, commonly referred to as stones within the renal system, and poses significant health challenges. Calcium phosphate and calcium oxalate are the predominant constituents of renal calculi and are introduced into the human body primarily via dietary sources. The presence of oxalates can become particularly problematic when the delicate balance of the normal flora residing within the gastrointestinal tract is disrupted. Within the human gut, species of Oxalobacter, Lactobacillus, and Bifidobacterium coexist in a symbiotic relationship. They play a pivotal role in mitigating the risk of stone formation by modulating certain biochemical pathways and producing specific enzymes that can facilitate the breakdown and degradation of oxalate salts. The probiotic potential exhibited by these bacteria is noteworthy, as it underscores their possible utility in the prevention of nephrolithiasis. Investigating the mechanisms by which these beneficial microorganisms exert their effects could lead to novel therapeutic strategies aimed at reducing the incidence of kidney stones. The implications of utilizing probiotics as a preventive measure against kidney stone formation represent an intriguing frontier in both nephrology and microbiome research, meriting further investigation to unlock their full potential.

Gut Microbiota and Metabolic Alterations Associated with Heart Failure and Coronary Artery Disease

This study investigates the role of gut microbiota in cardiovascular diseases, with an additional focus on pro-atherogenic metabolites. We use advanced network analysis and machine learning techniques to identify key microbial features linked to coronary artery disease (CAD) and heart failure with reduced ejection fraction (HFrEF). This cross-sectional study included 189 participants divided into three groups: coronary artery disease (n = 93), heart failure with reduced ejection fraction (n = 43), and controls (n = 53). Assessments included physical exams, echocardiography, dietary surveys, blood analysis, and fecal analysis. Gut microbiota composition was analyzed using next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR). Statistical analysis methods for testing hypotheses and correlations, alpha and beta-diversity analyses, co-occurrence networks, and machine learning were conducted using Python libraries or R packages with multiple comparisons corrected using the Benjamini-Hochberg procedure. Significant gut microbiota alterations were observed, with higher Bacillota/Bacteroidota ratios in CAD and HFrEF groups compared to controls (p < 0.001). Significant differences were observed in α-diversity indices (Pielou, Chao1, Faith) between disease groups and controls (p < 0.001). β-diversity analyses also revealed distinct microbial profiles (p = 0.0015). Interestingly, trimethylamine N-oxide (TMAO) levels were lower in CAD and HFrEF groups compared to controls (p < 0.05), while indoxyl sulfate (IS) levels were comparable between the study groups. Co-occurrence network analysis and machine learning identified key microbial features linked to these conditions, highlighting complex interactions within the gut microbiota associated with cardiovascular disease.

Fei-Yan-Qing-Hua decoction attenuates influenza virus infection by enhancing host antiviral response through microbiota-derived acetate

Background

Fei-Yan-Qing-Hua decoction (FYQHD) is derived from the well-known Ma Xing Shi Gan decoction, which was documented in Zhang Zhong Jing's "Treatise on Exogenous Febrile Disease" during the Han Dynasty. Although FYQHD has been used in the treatment of pneumonia and has demonstrated clinical efficacy for decades, the underlying mechanism by which FYQHD protects against influenza virus infection through modulation of gut flora remains unclear. Here, we examined the regulatory impacts of FYQHD on an influenza virus-infected mouse model and explored the mechanisms involved.

Methods

An infectious mouse model was created by intranasal instillation of influenza A virus (IAV). The effectiveness of FYQHD was assessed through various measures, including weight loss, lung wet/dry ratio, oxidative stress levels, viral load in lung tissues, and intestinal injuries. Changes in gut microbiota and SCFA production were also examined.

Results

The results showed that FYQHD significantly reduced viral load, increased the production of type I interferon (IFN-I), and restored the integrity of the intestinal barrier following IAV challenge. Additionally, FYQHD significantly corrected the dysbiosis of gut microbiota induced by influenza virus infection, enhancing the abundance of SCFA-producing bacteria and acetate production. However, the depletion of gut microbiota significantly attenuated the protective effects of FYQHD against influenza virus infection. In vitro, the antiviral effect of acetate was demonstrated through the upregulation of concentrations of IFN-β.

Conclusion

FYQHD attenuates influenza virus-induced lung and intestinal injuries by boosting the host antiviral response through increasing the abundance of Lachnospiraceae_NK4A136 and Roseburia, along with elevated acetate levels. The study advances our understanding of the therapeutic mechanisms of FYQHD and provides a theoretical basis for the application of FYQHD in the treatment of influenza.

Gut Microbiota and Polycystic Ovary Syndrome (PCOS): Understanding the Pathogenesis and the Role of Probiotics as a Therapeutic Strategy

Polycystic ovary syndrome (PCOS) is one of the most common disorders among women in modern societies. A variety of factors can contribute to the development of PCOS. These women often exhibit high insulin resistance (IR), hyperandrogenism, irregular periods, and infertility. Dysbiosis of the gut microbiota (GMB) in women with PCOS has attracted the attention of many researchers. Porphyromonas spp., B. coprophilus, and F. prausnitzii are found in higher numbers in the gut of women with PCOS. Short-chain fatty acids (SCFAs), produced by the intestinal microbiota through fermentation, play an essential role in regulating metabolic activities and are helpful in reducing insulin resistance and improving PCOS symptoms. According to studies, the bacteria producing SCFAs in the gut of these women are less abundant than in healthy women. The effectiveness of using probiotic supplements has been proven to improve the condition of women with PCOS. Daily consumption of probiotics improves dysbiosis of the intestinal microbiome and increases the production of SCFAs.

Intestinal microbiota diversity from broilers with runting and stunting syndrome performed by metagenomics

Runting and stunting syndrome (RSS) is an enteric viral disease in commercial poultry that directly affects gut health; however, its influence on gut microbiota remains unknown. This study aimed to investigate the compositional changes in the bacterial community of the ileum of 7-day-old broiler chicks naturally affected or not affected by RSS, using next-generation sequencing (NGS) technology. Twenty-one samples were obtained from the ileal contents and mucosa of 11 chicks with RSS and 10 healthy chicks, raised in a dark house system located on a farm in the state of Minas Gerais, Brazil. The results revealed overall changes in the gut microbiota of the chicks with RSS, including a decrease in microbial richness and diversity. In particular, there was a decrease in Lactobacillus and an increase in Candidatus Arthromitus and Clostridium sensu stricto 1. These results indicate a relationship between viral infection and the gut microbial composition, which can cause gut dysbiosis and may influence inflammation in this organ.RESEARCH HIGHLIGHTS RSS causes dysbiosis of the gut microbiota of the ilea of chicks.A difference was found in gut microbiota between chicks with or without RSS.Candidatus Arthromitus was predominant in chicks with RSS.Clostridium sensu stricto 1 was strictly associated with chicks with RSS.

Efficient reduction of antibiotic resistance genes and mobile genetic elements in organic waste composting via fenton-like treatment

Livestock manure harbors antibiotic resistance genes (ARGs), and aerobic composting (AC) is widely adopted for waste management. However, mitigating ARG resurgence in later stages remains challenging. This work aims to curb ARGs rebounding through a Fenton-like reaction during food waste and swine manure co-composting. Results revealed that 0.025 % zerovalent iron (ZVI) + 0.5 % hydrogen peroxide (H2O2) facilitated maximum ARG, mobile genetic elements (MGEs), and 16 s rRNA removal with reductions of 2.68, 2.69, and 1.4 logs. Spectroscopic analysis confirmed Fenton-like reaction and cell apoptosis analysis indicated that 0.025 % ZVI and 0.5 % H2O2 treatment had the maximum early apoptosis, least observed, and normal cells on day 30. Redundancy analysis highlighted the influence of bacterial communities and physicochemical properties on ARGs, with MGEs playing a crucial role in Fenton treatments. Our findings suggest incorporating ZVI and H2O2 in composting can significantly reduce ARGs and enhance waste management practices.

Gut mucosal microbiota profiles linked to development of positional-specific human colorectal cancer

Colorectal cancer (CRC) continuously ranks as the third most common cause of cancer-related deaths worldwide. Based on anatomical classifications and clinical diagnoses, CRC is classified into right-sided, left-sided, and rectal CRC. Importantly, the three types of positional-specific CRC affect the prognosis outcomes, thus indicating that positional-specific treatments for CRC are required. Emerging evidence suggests that besides host genetic and epigenetic alterations, gut mucosal microbiota is linked to gut inflammation, CRC occurrence, and prognoses. However, gut mucosal microbiota associated with positional-specific CRC are poorly investigated. Here, we report the gut mucosal microbiota profiles associated with these three types of CRC. Our analysis showed that the unique composition and biodiversity of bacterial taxa are linked to positional-specific CRC. We found that a combination of bacterial taxa can serve as potential biomarkers to distinguish the three types of CRC. Further investigations of the physiological roles of bacteria associated with positional-specific CRC may help understand the mechanism of CRC progression in different anatomical locations under the impact of gut mucosal microbiota.

Functional Muffins Exert Bifidogenic Effects along with Highly Product-Specific Effects on the Human Gut Microbiota Ex Vivo

GoodBiome™ Foods are functional foods containing a probiotic (Bacillus subtilis HU58™) and prebiotics (mainly inulin). Their effects on the human gut microbiota were assessed using ex vivo SIFR® technology, which has been validated to provide clinically predictive insights. GoodBiome™ Foods (BBM/LCM/OSM) were subjected to oral, gastric, and small intestinal digestion/absorption, after which their impact on the gut microbiome of four adults was assessed (n = 3). All GoodBiome™ Foods boosted health-related SCFA acetate (+13.1/14.1/13.8 mM for BBM/LCM/OSM), propionate (particularly OSM; +7.4/7.5/8.9 mM for BBM/LCM/OSM) and butyrate (particularly BBM; +2.6/2.1/1.4 mM for BBM/LCM/OSM). This is related to the increase in Bifidobacterium species (B. catenulatum, B. adolescentis, B. pseudocatenulatum), Coprococcus catus and Bacteroidetes members (Bacteroides caccae, Phocaeicola dorei, P. massiliensis), likely mediated via inulin. Further, the potent propionogenic potential of OSM related to increased Bacteroidetes members known to ferment oats (s key ingredient of OSM), while the butyrogenic potential of BBM related to a specific increase in Anaerobutyricum hallii, a butyrate producer specialized in the fermentation of erythritol (key ingredient of BBM). In addition, OSM/BBM suppressed the pathogen Clostridioides difficile, potentially due to inclusion of HU58™ in GoodBiome™ Foods. Finally, all products enhanced a spectrum of metabolites well beyond SCFA, including vitamins (B3/B6), essential amino acids, and health-related metabolites such as indole-3-propionic acid. Overall, the addition of specific ingredients to complex foods was shown to specifically modulate the gut microbiome, potentially contributing to health benefits. Noticeably, our findings contradict a recent in vitro study, underscoring the critical role of employing a physiologically relevant digestion/absorption procedure for a more accurate evaluation of the microbiome-modulating potential of complex foods.

Role of the intestinal microbiota in contributing to weight disorders and associated comorbidities

SUMMARYThe gut microbiota is a major factor contributing to the regulation of energy homeostasis and has been linked to both excessive body weight and accumulation of fat mass (i.e., overweight, obesity) or body weight loss, weakness, muscle atrophy, and fat depletion (i.e., cachexia). These syndromes are characterized by multiple metabolic dysfunctions including abnormal regulation of food reward and intake, energy storage, and low-grade inflammation. Given the increasing worldwide prevalence of obesity, cachexia, and associated metabolic disorders, novel therapeutic strategies are needed. Among the different mechanisms explaining how the gut microbiota is capable of influencing host metabolism and energy balance, numerous studies have investigated the complex interactions existing between nutrition, gut microbes, and their metabolites. In this review, we discuss how gut microbes and different microbiota-derived metabolites regulate host metabolism. We describe the role of the gut barrier function in the onset of inflammation in this context. We explore the importance of the gut-to-brain axis in the regulation of energy homeostasis and glucose metabolism but also the key role played by the liver. Finally, we present specific key examples of how using targeted approaches such as prebiotics and probiotics might affect specific metabolites, their signaling pathways, and their interactions with the host and reflect on the challenges to move from bench to bedside.

Re-framing the importance of Group B Streptococcus as a gut-resident pathobiont

Streptococcus agalactiae (Group B Streptococcus, GBS) is a Gram-positive bacterial species that causes disease in humans across the lifespan. While antibiotics are used to mitigate GBS infections, it is evident that antibiotics disrupt human microbiomes (which can predispose people to other diseases later in life), and antibiotic resistance in GBS is on the rise. Taken together, these unintended negative impacts of antibiotics highlight the need for precision approaches for minimizing GBS disease. One possible approach involves selectively depleting GBS in its commensal niches before it can cause disease at other body sites or be transmitted to at-risk individuals. One understudied commensal niche of GBS is the adult gastrointestinal (GI) tract, which may predispose colonization at other body sites in individuals at risk for GBS disease. However, a better understanding of the host-, microbiome-, and GBS-determined variables that dictate GBS GI carriage is needed before precise GI decolonization approaches can be developed. In this review, we synthesize current knowledge of the diverse body sites occupied by GBS as a pathogen and as a commensal. We summarize key molecular factors GBS utilizes to colonize different host-associated niches to inform future efforts to study GBS in the GI tract. We also discuss other GI commensals that are pathogenic in other body sites to emphasize the broader utility of precise de-colonization approaches for mitigating infections by GBS and other bacterial pathogens. Finally, we highlight how GBS treatments could be improved with a more holistic understanding of GBS enabled by continued GI-focused study.

Beneficial Bacteria in the Gut Microbiota May Lead to Improved Metabolic and Immunological Status in Chronic Obstructive Pulmonary Disease

The progression of chronic obstructive pulmonary disease (COPD) is characterized by functional changes in the airways. The lung-gut axis and gut microbiota (GM) have been linked to the pathophysiology of airway diseases. Regarding COPD, studies have shown that GM alterations could be related the stages of this disease. However, the relationship between GM and clinical, biochemical and immunological parameters in patients with COPD are not well understood. The aim of this study was to compare the relative abundance of specific groups of beneficial gut bacteria between COPD patients and healthy controls (CTLs) in order to evaluate relationships with metabolic and inflammatory markers in COPD.

METHODS

We included 16 stable COPD patients and 16 healthy volunteer CTLs. The relative abundances of Bifidobacterium spp. (Bf) and Akkermansia muciniphila (Akk) bacteria and the Bacteroidetes and Firmicutes phyla were assessed by qPCR. Pulmonary function was evaluated by spirometry, biochemical parameters by colorimetric methods and plasma cytokine levels by cytometric bead array analysis.

RESULTS

The Firmicutes/Bacteroides ratio was related to emergency hospital visits and six-minute walk test (6MWT) results. Furthermore, the relative abundance of Bf was associated with plasma concentrations of glucose, triglycerides, HDL-C and IL-10. In addition, Firmicutes levels and the Firmicutes/Bacteroidetes ratio were associated with the IL-12/IL-10 ratio, while Akk abundance was linked to IL-12 levels.

CONCLUSIONS

The present findings suggest that the abundance of beneficial bacteria in the GM could influence clinical presentation and immunoregulation in COPD.

The microbiota: a crucial mediator in gut homeostasis and colonization resistance

The gut microbiota is a complex and diverse community of microorganisms that colonizes the human gastrointestinal tract and influences various aspects of human health. These microbes are closely related to enteric infections. As a foreign entity for the host, commensal microbiota is restricted and regulated by the barrier and immune system in the gut and contributes to gut homeostasis. Commensals also effectively resist the colonization of pathogens and the overgrowth of indigenous pathobionts by utilizing a variety of mechanisms, while pathogens have developed strategies to subvert colonization resistance. Dysbiosis of the microbial community can lead to enteric infections. The microbiota acts as a pivotal mediator in establishing a harmonious mutualistic symbiosis with the host and shielding the host against pathogens. This review aims to provide a comprehensive overview of the mechanisms underlying host-microbiome and microbiome-pathogen interactions, highlighting the multi-faceted roles of the gut microbiota in preventing enteric infections. We also discuss the applications of manipulating the microbiota to treat infectious diseases in the gut.

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

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

Individual virome analysis reveals the general co-infection of mammal-associated viruses with SARS-related coronaviruses in bats

Bats are the natural reservoir hosts for SARS-related coronavirus (SARSr-CoV) and other highly pathogenic microorganisms. Therefore, it is conceivable that an individual bat may harbor multiple microbes. However, there is limited knowledge on the overall co-circulation of microorganisms in bats. Here, we conducted a 16-year monitoring of bat viruses in south and central China and identified 238 SARSr-CoV positive samples across nine bat species from ten provinces or administrative districts. Among these, 76 individual samples were selected for further metagenomics analysis. We found a complex microenvironment characterized by the general co-circulation of microbes from two different sources: mammal-associated viruses or environment-associated microbes. The later includes commensal bacteria, enterobacteria-related phages, and insect or fungal viruses of food origin. Results showed that 25% (19/76) of the samples contained at least one another mammal-associated virus, notably alphacoronaviruses (13/76) such as AlphaCoV/YN2012, HKU2-related CoV and AlphaCoV/Rf-HuB2013, along with viruses from other families. Notably, we observed three viruses co-circulating within a single bat, comprising two coronavirus species and one picornavirus. Our analysis also revealed the potential presence of pathogenic bacteria or fungi in bats. Furthermore, we obtained 25 viral genomes from the 76 bat SARSr-CoV positive samples, some of which formed new evolutionary lineages. Collectively, our study reveals the complex microenvironment of bat microbiome, facilitating deeper investigations into their pathogenic potential and the likelihood of cross-species transmission.

Let food be your medicine - dietary fiber

Dietary fiber (DF) cannot be digested and absorbed by the digestive tract, nor can it provide the energy needed to be burned for metabolic activities. Therefore, from the 1950s to the 1980s, DF received little attention in nutrition studies. With in-depth research and developments in global nutrition, people have gradually paid attention to the fact that DF occupies an essential position in the structure of nutrition, and it can ensure the healthy development of human beings. As early as 390 B.C., the ancient Greek physician Hippocrates proposed, "Let your food be your medicine, and your medicine be your food". This concept has been more systematically validated in modern scientific research, with numerous epidemiological studies showing that the dietary intake of DF-rich foods such as whole grains, root vegetables, legumes, and fruits has the potential to regulate the balance of the gut microbiota and thereby prevent diseases. However, the crosstalk between different types of DF and the gut microbiota is quite complex, and the effects on the organism vary. In this paper, we discuss research on DF and the gut microbiota and related diseases, aiming to understand the relationship between all three better and provide a reference basis for the risk reduction of related diseases.

Gut Microbiota Composition Is Causally Linked to Multiple Sclerosis: A Mendelian Randomization Analysis

Accumulating evidence links the microbial communities inhabiting the gut to the pathophysiological processes underlying multiple sclerosis (MS). However, most studies on the microbiome in MS are correlative in nature, thus being at risk of confounding and reverse causality. Mendelian randomization (MR) analyses allow the estimation of the causal relationship between a risk factor and an outcome of interest using genetic variants as proxies for environmental exposures. Here, we performed a two-sample MR to assess the causality between the gut microbiome and MS. We extracted genetic instruments from summary statistics from three large genome-wide association studies (GWASs) on the gut microbiome (18,340, 8959, and 7738 subjects). The exposure data were derived from the latest GWAS on MS susceptibility (47,429 patients and 68,374 controls). We pinpointed several microbial strains whose abundance is linked with enhanced MS risk (Actinobacteria class, Bifidobacteriaceae family, Lactobacillus genus) or protection (Prevotella spp., Lachnospiranaceae genus, Negativibacillus genus). The largest risk effect was seen for Ruminococcus Torques (OR, 2.89, 95% C.I. 1.67-5, p = 1.51 × 10-4), while Akkermansia municiphila emerged as strongly protective (OR, 0.43, 95% C.I. 0.32-0.57, p = 1.37 × 10-8). Our findings support a causal relationship between the gut microbiome and MS susceptibility, reinforcing the relevance of the microbiome-gut-brain axis in disease etiology, opening wider perspectives on host-environmental interactions for MS prevention.