Fecal Microbiome Research Articles

Sexual Dimorphism in the Immunometabolic Role of Gpr183 in Mice

Abstract Aim Excessive eating and intake of a Western diet negatively affect the intestinal immune system, resulting in compromised glucose homeostasis and lower gut bacterial diversity. The G protein-coupled receptor GPR183 regulates immune cell migration and intestinal immune response and has been associated with tuberculosis, type 1 diabetes, and inflammatory bowel diseases. We hypothesized that with these implications, GPR183 has an important immunometabolic role and investigated this using a global Gpr183 knock-out mouse model. Material and methods Wild-type (WT) and Gpr183 deficient (Gpr183-/-) mice were fed a high-fat, high-sucrose diet (HFSD) for 15 weeks. We investigated changes in weight, body composition, fecal IgA levels, fecal microbiome, and glucose tolerance before and after the diet. Macrophage infiltration into visceral fat was determined by flow cytometry, and hepatic gene expression was measured. Results and conclusions A sexual dimorphism was discovered, where female Gpr183-/- mice showed adverse metabolic outcomes compared to WT counterparts with inferior glucose tolerance, lower fecal IgA levels, and increased macrophage infiltration in visceral fat. In contrast, male Gpr183-/- mice had significantly lower fasting blood glucose after diet than male WT mice. Liver gene expression showed reduced inflammation and macrophage markers in Gpr183-/- livers, regardless of sex, while the pancreatic islet area did not differ between the groups. No conclusive differences were found after microbiome sequencing. To conclude, Gpr183 maintains metabolic homeostasis in female but not in male mice independent of diet. If confirmed in humans, future therapy targeting GPR183 should consider this sexual dimorphism.

Fecal microbial marker panel for aiding diagnosis of autism spectrum disorders.

Accumulating evidence suggests that gut microbiota alterations influence brain function and could serve as diagnostic biomarkers and therapeutic targets. The potential of using fecal microbiota signatures to aid autism spectrum disorder (ASD) detection is still not fully explored. Here, we assessed the potential of different levels of microbial markers (taxonomy and genome) in distinguishing children with ASD from age and gender-matched typically developing peers (n = 598, ASD vs TD = 273 vs 325). A combined microbial taxa and metagenome-assembled genome (MAG) markers showed a better performance than either microbial taxa or microbial MAGs alone for detecting ASD. A machine-learning model comprising 5 bacterial taxa and 44 microbial MAG markers (2 viral MAGs and 42 bacterial MAGs) achieved an area under the receiving operator curve (AUROC) of 0.886 in the discovery cohort and 0.734 in an independent validation cohort. Furthermore, the identified biomarkers and predicted ASD risk score also significantly correlated with the core symptoms measured by the Social Responsiveness Scale-2 (SRS-2). The microbiome panel showed a superior classification performance in younger children (≤6 years old) with an AUROC of 0.845 than older children (>6 years). The model was broadly applicable to subjects across genders, with or without gastrointestinal tract symptoms (constipation and diarrhea) and with or without psychiatric comorbidities (attention deficit and hyperactivity disorder and anxiety). This study highlights the potential clinical validity of fecal microbiome to aid in ASD diagnosis and will facilitate studies to understand the association of disturbance of human gut microbiota and ASD symptom severity.

Unveiling the Gut Microbiome of Malaysia's Colobine Monkeys : Insights into Health and Evolution.

Colobines are primarily leaf-eating primates, depend on microbiota of gastrointestinal tracts for food digestion. However, the gut microbiota of Malaysia's colobines specifically langurs remains unstudied. Hence, we aim to analyze the fecal microbiomes of Malaysia's langurs using Presbytis femoralis, Presbytis robinsoni, Trachypithecus obscurus, and Trachypithecus cristatus from various landscapes as models. We collected samples from all four species across several areas in Peninsular Malaysia and performed 16S ribosomal RNA gene amplicon sequencing using the Illumina sequencing platform. Presbytis femoralis exhibited the highest bacterial diversity, followed by T. obscurus, T. cristatus, P. robinsoni and the lowest, P. siamensis. Over 11 million operational taxonomic units (OTUs) were identified across Malaysia's langurs spanning 26 phyla, 180 families, and 329 genera of microbes. The OTUs were dominated by Firmicutes, Proteobacteria, and Bacteroidetes. There are 11 genera of pathogenic bacteria were identified across all host species. Nine pathogenic bacterial genera inhabit both T. obscurus, indicating poor health due to low bacterial diversity and heightened pathogenicity. In contrast, P. robinsoni with the fewest pathogenic species is deemed the healthiest among Malaysia's langurs. This study demonstrates that alterations in diet, behavior, and habitat affect bacterial diversity in Malaysia's langurs' gut microbiota. Even though this is the first comprehensive analysis of langur microbiomes in Malaysia, it is important to note the limitations regarding the number of samples, populations sampled, and the geographical origins and landscapes of these populations. Our results suggest that Malaysia's langurs may harbor pathogenic bacteria, potentially posing a risk of transmission to humans. This highlights the critical need for the conservation and management of Malaysia's langurs, particularly considering their interactions with humans. This data can serve as a foundation for authorities to inform the public about the origins and significance of animal health and the management of zoonotic diseases.

Tryptophan Metabolites Improve Intestinal Mucosal Barrier via the Aryl Hydrocarbon Receptor-Interleukin-22 Pathway in Murine Dextran Sulfate Sodium-Induced Pouchitis.

Pouchitis is the commonest complication after ileal pouch-anal anastomosis for ulcerative colitis. The protective effect of tryptophan metabolites on the mucosal barrier may be an effective method for treating pouchitis. The role of tryptophan metabolites on pouchitis remained unclear. We aimed to establish a murine model of dextran sulfate sodium-induced pouchitis to examine the roles of tryptophan metabolites in its pathogenesis. This is a study combined clinical patient data and animal research. A total of 22 patients were enrolled: 5 with familial adenomatous polyposis after ileal pouch-anal anastomosis, eight ulcerative colitis patients after ileal pouch-anal anastomosis patients with pouchitis, and 9 ulcerative colitis patients after ileal pouch-anal anastomosis with normal pouch. The demographic data and fecal samples of patients were collected. Male C57BL/6 mice were purchased from a licensed breeder and underwent ileal pouch-anal anastomosis to establish murine model of pouch. The bloods, feces, tissues of mice were collected. This study was performed in an academic medical center in China. The demographic data of patients were observational collected. The mice underwent ileal pouch-anal anastomosis were divided into six groups: control group with chow diet, dextran sulfate sodium, 6-formylindolo[3,2-b] carbazole + dextran sulfate sodium, high tryptophan diet + dextran sulfate sodium, CH-223191 + dextran sulfate sodium, indole-3-carboxaldehyde + dextran sulfate sodium. Animals were sacrificed after dextran sulfate sodium for 7 days. Fecal tryptophan metabolite level and microbiome composition, the severity of pouchitis, intestinal mucosal barrier function, and activation of the aryl hydrocarbon receptor-interleukin 22 pathway were assessed. Patients with pouchitis had lower fecal microbial diversity and indole-3-acetic acid levels. In murine pouchitis model, high-tryptophan diet increased fecal levels of 3-indoleglyoxylic acid, indole-3-aldehyde, and indole. A high-tryptophan diet and intraperitoneal aryl hydrocarbon receptor ligand 6-formylindolo[3,2-b] carbazole injection alleviated pouchitis. Tryptophan metabolites improved pouch mucosal barriers. aryl hydrocarbon receptor inhibitors exacerbated experimental pouchitis and disrupted the mucosal barrier; however, the aryl hydrocarbon receptor ligand indole-3-carboxaldehyde reversed this effect. This study was limited by small human sample size and lacking an Aryl hydrocarbon receptor knockout mouse model. A high-tryptophan diet and aryl hydrocarbon receptor ligand alleviated dextran sulfate sodium-induced pouchitis in murine ileal pouch-anal anastomosis model, which might be through regulating epithelial tight junctions and promoting goblet-cell differentiation, as well as maintaining the integrity and function of the mucosal barrier. This study provides a rationale for the clinical application of Aryl hydrocarbon receptor ligands in the treatment of pouchitis. See Video Abstract.

Isomalto-Oligosaccharide Potentiates Alleviating Effects of Intermittent Fasting on Obesity-Related Cognitive Impairment during Weight Loss and the Rebound Weight Gain.

Obesity-related cognitive dysfunction poses a significant threat to public health. The present study demonstrated mitigating effects of intermittent fasting (IF) and its combination with isomalto-oligosaccharides and IF (IF + IMO) on cognitive impairments induced by a high-fat-high-fructose (HFHF) diet in mice, with IF + IMO exhibiting superior effects. Transcriptomic analysis of the hippocampus revealed that the protective effects on cognition might be attributed to the suppression of toll-like receptor 4 (TLR4)/NFκB signaling, oxidative phosphorylation, and neuroinflammation. Moreover, both IF and IF + IMO modulated the gut microbiome and promoted the production of short-chain fatty acids, with IF + IMO displaying more pronounced effects. IF + IMO-modulated gut microbiota, metabolites, and molecular targets associated with cognitive impairments were further corroborated using human data from public databases Gmrepo and gutMgene. Furthermore, the fecal microbiome transplantation confirmed the direct impacts of IF + IMO-derived microbiota on improving cognition functions by suppressing TLR4/NFκB signaling and increasing BDNF levels. Notably, prior exposure to IF + IMO prevented weight-regain-induced cognitive decline, suppressed TLR4/NFκB signaling and inflammatory cytokines in the hippocampus, and mitigated weight regain-caused gut dysbacteriosis without altering body weight. Our study underscores that IMO-augmented alleviating effects of IF on obesity-related cognitive impairment particularly during weight-loss and weight-regain periods, presenting a novel nutritional strategy to tackle obesity-related neurodegenerative disorders.

Aging-induced dysbiosis worsens sepsis severity but is attenuated by probiotics in D-galactose-administered mice with cecal ligation and puncture model.

Despite the well-established effects of aging on brain function and gut dysbiosis (an imbalance in gut microbiota), the influence of aging on sepsis-associated encephalopathy (SAE) and the role of probiotics in this context remain less understood. C57BL/6J mice (8-week-old) were subcutaneously administered with 8 weeks of D-galactose (D-gal) or phosphate buffer solution (PBS) for aging and non-aging models, respectively, with or without 8 weeks of oral Lacticaseibacillus rhamnosus GG (LGG). Additionally, the impact of the condition media from LGG (LCM) was tested in macrophages (RAW 264.7 cells), microglia (BV-2 cells), and hippocampal cells (HT-22 cells). Fecal microbiome analysis demonstrated D-gal-induced dysbiosis (reduced Firmicutes and Desulfobacterota with increased Bacteroidota and Verrucomicrobiota), which LGG partially neutralized the dysbiosis. D-gal also worsens cecal ligation and puncture (CLP) sepsis severity when compared with PBS-CLP mice, as indicated by serum creatinine (Scr) and alanine transaminase (ALT), but not mortality, neurological characteristics (SHIRPA score), and serum cytokines (TNF-α and IL-6). Additionally, D-gal-induced aging was supported by fibrosis in the liver, kidney, and lung; however, CLP sepsis did not worsen fibrosis. Interestingly, LGG attenuated all parameters (mortality, Scr, ALT, SHIRPA, and cytokines) in non-aging sepsis (PBS-CLP) while improving all these parameters, except for mortality and serum IL-6, in aging sepsis (D-gal CLP). For the in vitro test using lipopolysaccharide (LPS) stimulation, LCM attenuated inflammation in some parameters on RAW264.7 cells but not BV-2 and HT-22 cells, implying a direct anti-inflammatory effect of LGG on macrophages, but not in cells from the brain. D-gal induced fecal dysbiosis and worsened sepsis severity as determined by Scr and ALT, and LGG could alleviate most of the selected parameters of sepsis, including SAE. However, the impact of LGG on SAE was not a direct delivery of beneficial molecules from the gut to the brain but partly due to the attenuation of systemic inflammation through the modulation of macrophages.

Alterations of the gut microbiome in HIV infection highlight human anelloviruses as potential predictors of immune recovery

BackgroundHIV-1 infection is characterized by a massive depletion of mucosal CD4 T cells that triggers a cascade of events ultimately linking gut microbial dysbiosis to HIV-1 disease progression and pathogenesis. The association between HIV infection and the enteric virome composition is less characterized, although viruses are an essential component of the gut ecosystem. Here, we performed a cross-sectional analysis of the fecal viral (eukaryotic viruses and bacteriophages) and bacterial microbiome in people with HIV (PWH) and in HIV-negative individuals. To gain further insight into the association between the gut microbiome composition, HIV-associated immunodeficiency, and immune recovery, we carried out a longitudinal study including 14 PWH who initiated antiretroviral therapy (ART) and were followed for 24 months with samplings performed at baseline (before ART) and at 2, 6, 12, and 24 months post-ART initiation.ResultsOur data revealed a striking expansion in the abundance and prevalence of several human virus genomic sequences (Anelloviridae, Adenoviridae, and Papillomaviridae) in stool samples of PWH with severe immunodeficiency (CD4 < 200). We also noted a decreased abundance of sequences belonging to two plant viruses from the Tobamovirus genus, a reduction in bacterial alpha diversity, and a decrease in Inoviridae bacteriophage sequences. Short-term ART (24 months) was linked to a significant decrease in human Anelloviridae sequences. Remarkably, the detection of Anellovirus sequences at baseline independently predicted poor immune recovery, as did low CD4 T cell counts. The bacterial and bacteriophage populations were unique to each PWH with individualized trajectories; we found no discernable pattern of clustering after 24 months on ART.ConclusionAdvanced HIV-1 infection was associated with marked alterations in the virome composition, in particular a remarkable expansion of human anelloviruses, with a gradual restoration after ART initiation. In addition to CD4 T cell counts, anellovirus sequence detection might be useful to predict and monitor immune recovery. This study confirms data on the bacteriome and expands our knowledge on the viral component of the gut microbiome in HIV-1 infection.3oR8qDfXoWY9s_P5ES648YVideo

Aged Gut Microbiome Induces Metabolic Impairment and Hallmarks of Vascular and Intestinal Aging in Young Mice.

Aging, an independent risk factor for cardiometabolic diseases, refers to a progressive deterioration in physiological function, characterized by 12 established hallmarks. Vascular aging is driven by endothelial dysfunction, telomere dysfunction, oxidative stress, and vascular inflammation. This study investigated whether aged gut microbiome promotes vascular aging and metabolic impairment. Fecal microbiome transfer (FMT) was conducted from aged (>75 weeks old) to young C57BL/6 mice (8 weeks old) for 6 weeks. Wire myography was used to evaluate endothelial function in aortas and mesenteric arteries. ROS levels were measured by dihydroethidium (DHE) staining and lucigenin-enhanced chemiluminescence. Vascular and intestinal telomere function, in terms of relative telomere length, telomerase reverse transcriptase expression and telomerase activity, were measured. Systemic inflammation, endotoxemia and intestinal integrity of mice were assessed. Gut microbiome profiles were studied by 16S rRNA sequencing. Some middle-aged mice (40-42 weeks old) were subjected to chronic metformin treatment and exercise training for 4 weeks to evaluate their anti-aging benefits. Six-week FMT impaired glucose homeostasis and caused vascular dysfunction in aortas and mesenteric arteries in young mice. FMT triggered vascular inflammation and oxidative stress, along with declined telomerase activity and shorter telomere length in aortas. Additionally, FMT impaired intestinal integrity, and triggered AMPK inactivation and telomere dysfunction in intestines, potentially attributed to the altered gut microbial profiles. Metformin treatment and moderate exercise improved integrity, AMPK activation and telomere function in mouse intestines. Our data highlight aged microbiome as a mechanism that accelerates intestinal and vascular aging, suggesting the gut-vascular connection as a potential intervention target against cardiovascular aging and complications.

Insights into the Gut Microbial Diversity of Wild Siberian Musk Deer (Moschus moschiferus) in Republic of Korea.

The gut microbiota plays a crucial role in the health and well-being of wildlife. However, its composition and diversity remain unexplored, particularly in threatened species such as the Siberian musk deer (SMD). This study aimed to elucidate the gut microbiota composition within different wild SMD communities for assessing their health status. We conducted the first comprehensive fecal microbiome analysis of wild SMD inhabiting three distinct locations in Gangwon Province, Republic of Korea (Korea). Fecal samples were collected non-invasively and 16S rRNA gene sequencing was performed for gut microbiota characterization. Consistent with previous research, Firmicutes and Bacteroidetes were the dominant phyla in the gut microbiota of wild SMD. Planctomycetota was a prevalent phylum in wild SMD gut microbiota, warranting further investigation of its ecological significance. While significant differences were observed in the gut microbiota richness among the three groups, no significant disparities were detected in the beta diversity. Additionally, certain genera exhibited distinct relative abundances among the groups, suggesting potential associations with geographic factors, gut disorders, and dietary habits. Our findings provide valuable insights into the gut microbiome of wild SMD and offer a foundation for future microbiome-based conservation efforts for this vulnerable species.

Fecal microbiome analysis uncovers hidden stress effects of low stocking density on rainbow trout

BackgroundRecirculating aquaculture systems can cause chronic stress in fish when stocking density is too high. However, this study tested whether low stocking density can cause fish stress. Adult rainbow trout, with an average weight of 1.517 kg (± 0.39), were subjected to low (12 kg/m3 ± 0.94) and moderate (43 kg/m3 ± 2.03) stocking densities for 24 days in a recirculating system maintained at 15 °C. At the end of the experiment, fecal microbiome analysis was carried out using a 16S rRNA amplicon sequencing. Additionally, an untargeted plasma metabolomics analysis was conducted.ResultsThe moderate stocking density group harboured greater numbers of commensals, such as C. somerae, R. lituseburensis, and L. plantarum. In contrast, detrimental species such as S. putrifacens and P. putida were abundant in the low-stocking density fish. Functional microbiome profiling revealed vitamin B12 salvage and synthesis in moderate stocking densities, which may support intestinal tight junction function. Additionally, vitamin B1 biosynthesis pathways were more abundant in the moderate stocking density group, which may function towards oxidative energy metabolism and protect against oxidative stress. A complementary plasma metabolomics study, although done at slightly different stocking densities and duration, confirmed the presence of blood metabolic stress markers. Elevated levels of L-lactic acid and L-Norvaline, L-Valine, and L-glutamine, indicate low stocking density fish were under stress. Furthermore, a P4HA2 stress gene biomarker confirmed the occurrence of stress in low-density fish. This study suggests that low stocking density can induce stress in fish. Moreover, moderate stocking density leads to a distinct and beneficial fecal microbiome profile.ConclusionOur study highlights the potential benefits of optimizing the stocking density of fish in recirculating aquaculture systems. This can improve fish health and welfare, promoting a more resilient fecal microbiome.Graphical abstract

Exogenous ketones exert antiseizure effects and modulate the gut microbiome and mycobiome in a clinically relevant murine model of epilepsy.

Despite growing interest in the potential use of exogenous ketones for the treatment of epilepsy, their impact on seizures and the gut microbiome and mycobiome remain unclear. Here, we examined the effects of both oral gavage and subcutaneous (SC) injection of a ketone ester (KE) in spontaneously epileptic Kcna1-null (KO) mice that model seminal aspects of human temporal lobe epilepsy. Electroencephalographic recordings and biochemical analyses were performed in KE-treated KO mice. Fecal microbial and fungal communities were profiled to determine whether the antiseizure activity of KE involves changes in the gut microbiome. We found that exogenous KE administration by SC injection was more effective than oral gavage in terms of rendering antiseizure effects while generating similar degrees of ketonemia. However, reductions in mean daily seizure counts were accompanied by overall alterations in the fecal bacterial microbiome. Either oral or SC injection imposed a greater impact on the microbiome in male than female mice. In males, oral KE decreased Bacteroidota phylum and genera of Ligilactobacillus and Muribaculaceae, whereas SC injection decreased Bacteroides, Lactobacillus, and Lachnospiraceae. The fecal mycobiome was affected by KE injection to a greater degree than by oral gavage, and more in females than in males, as reflected by an increase in Ascomycota and Saccharomyces. Correlation analysis between microbiome and seizure counts revealed that in mice receiving KE injection, the seizure count was positively correlated with an amplicon sequencing variant of Lactobacillus (Spearman rho = .64, p = .03) and tended toward a negative correlation with Saccharomyces (Spearman rho = -.57, p = .057). Our findings demonstrate that exogenous ketone administration alone can induce antiseizure effects equally via different routes of administration, and that they induce differential shifts in both the bacterial microbiome and mycobiome.

The influence of perilipin 5 deficiency on gut microbiome profiles in murine metabolic dysfunction-associated fatty liver disease (MAFLD) and MAFLD-hepatocellular carcinoma.

Metabolic dysfunction-associated fatty liver disease (MAFLD) has emerged as the leading cause of hepatocellular carcinoma (HCC) worldwide. Over the years, Perilipin 5 (PLIN5) has been recognized as a key regulator of both MAFLD and HCC development. In our previous studies we demonstrated that deficiency in Plin5 reduces the severity of MAFLD and HCC in mice. Interestingly, it has been established that patients with MAFLD and HCC exhibit various changes in their gut microbiome profiles. The gut microbiome itself has been shown to play a role in modulating carcinogenesis and the immune response against cancer. Therefore, we conducted a study to investigate the alterations in fecal microbiome composition in wild type (WT) and Plin5-deficient (Plin5 -/-) mice models of MAFLD and MAFLD-induced HCC (MAFLD-HCC). We utilized 16S rRNA gene sequencing analysis to profile the composition of gut bacteria in fecal samples. Notably, we discovered that the absence of Plin5 alone is already associated with changes in gut microbiota composition. Moreover, feeding the mice a Western diet (WD) resulted in additional microbial alterations. Interestingly, Plin5 -/- animals exhibited an enrichment of the beneficial taxa Lactobacillus in both animal models. Our findings identify Plin5 as a major regulator of gut microbiota during the development of MAFLD and MAFLD-HCC.

Dysbiosis index and fecal concentrations of sterols, long-chain fatty acids and unconjugated bile acids in dogs with inflammatory protein-losing enteropathy.

Canine protein-losing enteropathy (PLE) is a syndrome characterized by gastrointestinal loss of proteins. While fecal microbiome and metabolome perturbations have been reported in dogs with chronic enteropathy, they have not been widely studied in dogs with PLE. Therefore, the study aims were to investigate gut microbiome and targeted fecal metabolites in dogs with inflammatory PLE (iPLE) and evaluate whether treatment affects these changes at short-term follow-up. Thirty-eight dogs with PLE and histopathological evidence of gastrointestinal inflammation and 47 healthy dogs were enrolled. Fecal samples were collected before endoscopy (T0) and after one month of therapy (T1). Microbiome and metabolome alterations were investigated using qPCR assays (dysbiosis index, DI) and gas chromatography/mass spectrometry (long-chain fatty acids, sterols, unconjugated bile acids), respectively. Median (min-max) DI of iPLE dogs was 0.4 (-5.9 to 7.7) and was significantly higher (p < 0.0001) than median DI in healthy dogs [-2.0 (-6.0 to 5.3)]. No significant associations were found between DI and selected clinicopathological variables. DI did not significantly differ between T0 and T1. In iPLE dogs, at T0, myristic, palmitic, linoleic, oleic, cis-vaccenic, stearic, arachidonic, gondoic, docosanoic, erucic, and nervonic acids were significantly higher (p < 0.0001) than healthy dogs. In iPLE dogs, oleic acid (p = 0.044), stearic acid (p = 0.013), erucic acid (p = 0.018) and nervonic acid (p = 0.002) were significantly decreased at T1. At T0, cholesterol and lathosterol (p < 0.0001) were significantly higher in iPLE dogs compared to healthy dogs, while total measured phytosterols were significantly lower (p = 0.001). No significant differences in total sterols, total phytosterols and total zoosterols content were found at T1, compared to T0. At T0, total primary bile acids and total secondary bile acids did not significantly differ between healthy control dogs and iPLE dogs. No significant differences in fecal bile acid content were found at T1. Dysbiosis and lipid metabolism perturbations were observed in dogs with iPLE. Different therapeutic protocols lead to an improvement of some but not all metabolome perturbations at short-term follow-up.

Feeding of bakery products as replacement of cereal grains alter fecal microbiome and improve feed efficiency in fattening pigs

The re-integration of former foodstuffs, such as bakery products (BP), into pig feed reduces the feed-food competition and increases the sustainability of pig production. Nevertheless, there are concerns about the altered fatty acid profile in BP compared to standard diets and their effects on meat quality and the intestinal microbiome. The present study investigated the effects of replacing 30% cereal grains with BP in the diet on performance, microbiome composition and metabolites in feces of fattening pigs, economic aspects and meat quality characteristics. A total of 132 pigs (Large White × Piétrain; 11 weeks of age) were fed two diets containing 0 or 30% BP until reaching slaughter weight in three replicate batches. Fecal samples were collected for 16S rRNA amplicon sequencing after 6 weeks, whereas body fat samples were collected after 9 weeks on the diet. The results showed that BP can replace cereals in pig diets by up to 30% without impairing animal performance, while improving feed efficiency and reducing feed costs by 9% compared to the control. Additionally, pigs fed the BP diet had a 50%-higher n-3 fatty acid content in the neck and abdominal fat compared to the control. The improved feed efficiency in BP-fed pigs may be related to positive effects on the fecal microbiome, such as a higher alpha diversity and a reduction of fungi and yeasts. Our study provides valuable insights into the benefits of including BP in diets of fattening pigs, which should be investigated in future studies on other BP types.

Detection and characterization of Campylobacter in air samples from poultry houses using shot-gun metagenomics – a pilot study

BackgroundFoodborne pathogens such as Campylobacter jejuni are responsible for a large proportion of the gastrointestinal infections worldwide associated with poultry meat. Campylobacter spp. can be found in the chicken fecal microbiome and can contaminate poultry meat during the slaughter process. Commonly used sampling methods to detect Campylobacter spp. at poultry farms use fecal droppings or boot swabs in combination with conventional culture techniques or PCR. In this pilot study, we have used air filtering and filters spiked with mock communities in combination with shotgun metagenomics to detect Campylobacter and test the applicability of this approach for the detection and characterization of foodborne pathogens. To the best of our knowledge is this the first study that combines air filtering with shotgun metagenomic sequencing for detection and characterization of Campylobacter.ResultsAnalysis of air filters spiked with different levels of Campylobacter, into a background of mock or poultry house communities, indicated that we could detect as little as 200 colony forming units (CFU) Campylobacter per sample using our protocols. The results indicate that even with limited sequencing effort we could detect Campylobacter in the samples analysed in this study. We observed significant amounts of Campylobacter in real-life samples from poultry houses using both real-time PCR as well as shotgun metagenomics, suggesting that the flocks in both houses were infected with Campylobacter spp. Interestingly, in both houses we find diverse microbial communities present in the indoor air which reflect the fecal microbiome of poultry. Some of the identified genera such as Staphylococcus, Escherichia and Pseudomonas are known to contain opportunistic pathogenic species.ConclusionsThese results show that air sampling of poultry houses in combination with shotgun metagenomics can detect and identify Campylobacter spp. present at low levels. This is important since early detection of Campylobacter enables measures to be put in place to ensure the safety of broiler products, animal health and public health. This approach has the potential to detect any pathogen present in poultry house air.

Lactobacillus rhamnosus ameliorates experimental autoimmune neuritis via modulation of gut microbiota and metabolites

BackgroundGuillain-Barre syndrome (GBS), an autoimmune disease of the peripheral nervous system, is hallmarked by demyelination and immune cellular infiltration. Experimental autoimmune neuritis (EAN), considered a GBS prototype model, has been studied for its potential therapeutic benefits from lactobacilli. This study evaluated the protective role of Lactobacillus rhamnosus GG (GG) for treatment in EAN. T cell ratio, inflammation factors, sciatic nerve pathology, intestinal permeability, and gut inflammation were assessed on day 19 post-immunization to evaluate GG's effect on EAN. Fecal metabolomics and 16s rRNA microbiome analysis were conducted to elucidate its mechanism. ResultsGG dynamically balanced CD4+/CD8+T cell ratio, reduced serum IL-1β and TNF-α expression, improved sciatic nerve demyelination and inflammation, and enhanced neurological scores during peak disease period. Intestinal mucosal damage was evident in EAN rats, with downregulated Occludin and ZO-1 and upregulated IL-1β, TNF-α, and Reg3γ. GG treatment restored intestinal mucosal integrity, upregulated Occludin and ZO-1, and downregulated IL-1, TNF-α, and Reg3γ. GG partially rectified the gut microbiota and metabolite imbalance in EAN rats. ConclusionGG mitigates EAN through immune response modulation and inflammation reduction via the gut microbiota and metabolites.

Comparative analysis of the duodenojejunal microbiome with the oral and fecal microbiomes reveals its stronger association with obesity and nutrition

ABSTRACT The intestinal microbiota is increasingly recognized as a crucial player in the development and maintenance of various chronic conditions, including obesity and associated metabolic diseases. While most research focuses on the fecal microbiota due to its easier accessibility, the small intestine, as a major site for nutrient sensing and absorption, warrants further investigation to determine its microbiota composition and functions. Here, we conducted a clinical research project in 30 age- and sex-matched participants with (n = 15) and without (n = 15) obesity. Duodenojejunal fluid was obtained by aspiration during endoscopy. Phenotyping included clinical variables related to metabolic status, lifestyle, and psychosocial factors using validated questionnaires. We performed metagenomic analyses of the oral, duodenojejunal, and fecal microbiome, alongside metabolomic data from duodenojejunal fluid and feces, integrating these data with clinical and lifestyle information. Our results highlight significant associations between duodenojejunal microbiota composition and usual dietary intake, as well as clinical phenotypes, with larger effect sizes than the associations between these variables and fecal microbiota. Notably, we found that the duodenojejunal microbiota of patients with obesity exhibited higher diversity and showed distinct differences in the abundance of several duodenojejunal microbiota species compared with individuals without obesity. Our findings support the relevance of studying the role of the small intestinal microbiota in the pathogenesis of nutrition-related diseases.

Impact of Lyophilized Milk Kefir-Based Self-Nanoemulsifying System on Cognitive Enhancement via the Microbiota-Gut-Brain Axis.

Chronic inflammatory bowel disorders (IBDs) are characterized by altered intestinal permeability, prompting inflammatory, oxidative stress, and immunological factors. Gut microbiota disorders impact brain function via the bidirectional gut-brain axis, influencing behavior through inflammatory cascades, oxidative stress, and neurotransmitter levels. This study highlights the potential effect of integrating lyophilized milk kefir alone and lyophilized milk kefir as solid carriers loaded with a self-nanoemulsifying self-nanosuspension (SNESNS) of licorice extract on an induced chronic IBD-like model in rats. Licorice-SNESNS was prepared by the homogenization of 30 mg of licorice extract in 1 g of the selected SNEDDS (30% Caraway oil, 60% Tween 20, and 10% propylene glycol (w/w)). Licorice-SNESNS was mixed with milk kefir and then freeze-dried. Dynamic TEM images and the bimodal particle size curve confirmed the formation of the biphasic nanosystems after dilution (nanoemulsion and nanosuspension). Daily oral administration of lyophilized milk kefir (100 mg/kg) loaded with SNESNS (10 mg/kg Caraway oil and 1 mg/kg licorice) restored normal body weight and intestinal mucosa while significantly reducing submucosal inflammatory cell infiltration in induced rats. Importantly, this treatment demonstrated superior efficacy compared to lyophilized milk kefir alone by leading to a more significant alleviation of neurotransmitter levels and improved memory functions, thereby addressing gut-brain axis disorders. Additionally, it normalized fecal microbiome constituents, inflammatory cytokine levels, and oxidative stress in examined tissues and serum. Moreover, daily administration of kefir-loaded SNESNS normalized the disease activity index, alleviated histopathological changes induced by IBD induction, and partially restored the normal gut microbiota. These alterations are associated with improved cognitive functions, attributed to the maintenance of normal neurotransmitter levels and the alleviation of triggered inflammatory factors and oxidative stress levels.

Ultrafast metaproteomics for quantitative assessment of strain isolates and microbiomes

BackgroundMicrobial communities are essential in human health and environmental regulation, but present a challenge for the analytical science due to their diversity and dynamic range. Tandem mass spectrometry provides functional insights on microbial life cycle, but is time-consuming. MALDI TOF excels in rapid species identification, but not functional assessment. To address critical challenges in human health and environmental sustainability, microbiology needs advanced mass spectrometry methods and bioinformatic tools enabling both rapid identification and accurate assessment of functional activity of microbial communities. ResultsWe show for the first time that both identity and functional activity of microorganisms and their communities can be accurately determined in experiments as short as 7 min per sample, using the basic Orbitrap MS configuration without peptide fragmentation. The approach was validated using strain isolates, mock microbiomes composed of bacteria spiked at known concentrations and human fecal microbiomes. Our new bioinformatic algorithm identifies the bacterial species with an accuracy of 95 %, when no prior information on the sample is available. Microbiome composition was resolved at the genus level with the mean difference between the actual and identified components of 12 %. For mock microbiomes, Pearson coefficient of up to 0.97 was achieved in estimates of strain biomass change. By the example of Rhodococcus biodegradation of n-alkanes, phenols and its derivatives, we showed the accurate assessment of functional activity of strain isolates, compared with the standard label-free and label-based approaches. SignificanceOur approach makes microbial proteomics fast, functional and insightful using the Orbitrap instruments even without employing peptide fragmentation technology. The approach can be applied to any microorganisms and can take a niche in routine functional assessment of microbial pathogens and consortiums in clinical diagnostics together with MALDI TOF MS and 16S rRNA gene sequencing.

Performance, ruminal and fecal microbiome of lambs fed diets supplemented with probiotics.

The present study aimed to investigate the impact of adding two doses of a commercial probiotic on productive performance, ruminal and fecal microbiome in growing lambs. Forty-two Texel or Ile de France crossbred lambs aged 86.9 ± 8.0days (body weight: 27.4 ± 3.7kg) were distributed into three groups: basal diet without probiotic supplementation (CG); basal diet + 1g/animal/day of probiotic (GP1) and basal diet + 5g/animal/day of probiotic (GP5). The experimental period was 84days. The weight was evaluated weekly and dry matter intake (DMI) and leftovers were measured daily. At the end of the experiment, lambs were slaughtered. Feces and rumen fluid were collected for microbiome analysis and rumen fragments for histological evaluation. The use of probiotics did not affect weight gain, but GP1 showed a higher silage and DMI intake than CG (p < 0.001). The CG had a greater thickness of keratinized epithelium and stratum corneum (< 0.001) than GP1 and GP5, and greater total papilla width (p = 0.039) than GP1. There was no difference in the general abundance in the rumen and fecal microbiomes. GP5 had a higher proportion of Azoarcus and Dialister taxa in the rumen fluid (p = 0.012 and p = 0.017, respectively) and higher proportion of Treponema and Fibrobacter taxa in the fecal microbiome (p = 0.015 and p = 0.026, respectively), whereas CG had a higher proportion of Anaeroplasma than the other groups (p = 0.032). These results demonstrated the benefits of probiotics for ruminal epithelium protection and microbial diversity. However, there was no effect on performance parameters.