Gut Pathogens最新文献

{"title":"Urinary markers of Mycobacterium tuberculosis and dysbiosis in paediatric tuberculous meningitis cases undergoing treatment.","authors":"Simon Isaiah, Du Toit Loots, A Marceline Tutu van Furth, Elmarie Davoren, Sabine van Elsland, Regan Solomons, Martijn van der Kuip, Shayne Mason","doi":"10.1186/s13099-024-00609-9","DOIUrl":"10.1186/s13099-024-00609-9","url":null,"abstract":"<p><strong>Background: </strong>The pathogenesis of tuberculous meningitis (TBM) involves infection by Mycobacterium tuberculosis in the meninges and brain. However, recent studies have shown that the immune response and inflammatory processes triggered by TBM can have significant effects on gut microbiota. Disruptions in the gut microbiome have been linked to various systemic consequences, including altered immunity and metabolic dysregulation. Inflammation caused by TBM, antibiotic treatment, and changes in host immunity can all influence the composition of gut microbes. This complex relationship between TBM and the gut microbiome is of great importance in clinical settings. To gain a deeper understanding of the intricate interactions between TBM and the gut microbiome, we report innovative insights into the development of the disease in response to treatment. Ultimately, this could lead to improved outcomes, management strategies and quality of life for individuals affected by TBM.</p><p><strong>Method: </strong>We used a targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach to investigate metabolites associated with gut metabolism in paediatric participants by analysing the urine samples collected from a control group (n = 40), and an experimental group (n = 35) with confirmed TBM, which were subdivided into TBM stage 1 (n = 8), stage 2 (n = 11) and stage 3 (n = 16).</p><p><strong>Findings: </strong>Our metabolomics investigation showed that, of the 78 initially selected compounds of microbiome origin, eight unique urinary metabolites were identified: 2-methylbutyrlglycine, 3-hydroxypropionic acid, 3-methylcrotonylglycine, 4-hydroxyhippuric acid, 5-hydroxyindoleacetic acid, 5-hydroxyhexanoic acid, isobutyrylglycine, and phenylacetylglutamine as urinary markers of dysbiosis in TBM.</p><p><strong>Conclusion: </strong>These results - which are supported by previous urinary studies of tuberculosis - highlight the importance of gut metabolism and of identifying corresponding microbial metabolites as novel points for the foundation of improved management of TBM patients.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":"16 1","pages":"14"},"PeriodicalIF":4.3,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10936073/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140109765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A case–control study of the association between the gut microbiota and colorectal cancer: exploring the roles of diet, stress, and race","authors":"Tiffany L. Carson, Doratha A. Byrd, Kristen S. Smith, Daniel Carter, Maria Gomez, Michael Abaskaron, Rebecca B. Little, Sh’Nese Townsend Holmes, William J. van Der Pol, Elliot J. Lefkowitz, Casey D. Morrow, Andrew D. Fruge","doi":"10.1186/s13099-024-00608-w","DOIUrl":"https://doi.org/10.1186/s13099-024-00608-w","url":null,"abstract":"The gut microbiota is associated with risk for colorectal cancer (CRC), a chronic disease for which racial disparities persist with Black Americans having a higher risk of CRC incidence and mortality compared to other groups. Given documented racial differences, the gut microbiota may offer some insight into previously unexplained racial disparities in CRC incidence and mortality. A case–control analysis comparing 11 women newly diagnosed with CRC with 22 cancer-free women matched on age, BMI, and race in a 1:2 ratio was conducted. Information about participants’ diet and perceived stress levels were obtained via 24-h Dietary Recall and Perceived Stress Scale-10 survey, respectively. Participants provided stool samples from which microbial genomic DNA was extracted to reveal the abundance of 26 genera chosen a priori based on their previously observed relevance to CRC, anxiety symptoms, and diet. Significantly lower alpha diversity was observed among cancer-free Black women compared to all other race-cancer status combinations. No group differences were observed when comparing beta diversity. Non-Hispanic White CRC cases tended to have higher relative abundance of Fusobacteria, Gemellaceae, and Peptostreptococcus compared to all other race-cancer combination groups. Perceived stress was inversely associated with alpha diversity and was associated with additional genera. Our findings suggest that microbiome-CRC associations may differ by racial group. Additional large, racially diverse population-based studies are needed to determine if previously identified associations between characteristics of the gut microbiome and CRC are generalizable to Black women and other racial, ethnic, and gender groups.","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":"156 1","pages":""},"PeriodicalIF":4.2,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140099695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of enterotype and its predictive value for patients with colorectal cancer","authors":"Li Qingbo, Zhuang Jing, Qu Zhanbo, Chu Jian, Song Yifei, Wu Yinhang, Han Shuwen","doi":"10.1186/s13099-024-00606-y","DOIUrl":"https://doi.org/10.1186/s13099-024-00606-y","url":null,"abstract":"Gut microbiota dysbiosis involved in the pathogenesis of colorectal cancer (CRC). The characteristics of enterotypes in CRC development have not been determined. To characterize the gut microbiota of healthy, adenoma, and CRC subjects based on enterotype. The 16 S rRNA sequencing data from 315 newly sequenced individuals and three previously published datasets were collected, providing total data for 367 healthy, 320 adenomas, and 415 CRC subjects. Enterotypes were analyzed for all samples, and differences in microbiota composition across subjects with different disease states in each enterotype were determined. The predictive values of a random forest classifier based on enterotype in distinguishing healthy, adenoma, and CRC subjects were evaluated and validated. Subjects were classified into one of three enterotypes, namely, Bacteroide- (BA_E), Blautia- (BL_E), and Streptococcus- (S_E) dominated clusters. The taxonomic profiles of these three enterotypes differed among the healthy, adenoma, and CRC cohorts. BA_E group was enriched with Bacteroides and Blautia; BL_E group was enriched by Blautia and Coprococcus; S_E was enriched by Streptococcus and Ruminococcus. Relative abundances of these genera varying among the three human cohorts. In training and validation sets, the S_E cluster showed better performance in distinguishing among CRC patients, adenoma patients, and healthy controls, as well as between CRC and non-CRC individuals, than the other two clusters. This study provides the first evidence to indicate that changes in the microbial composition of enterotypes are associated with disease status, thereby highlighting the diagnostic potential of enterotypes in the treatment of adenoma and CRC. Three enterotypes (BA_E, BL_E, and S_E) were identified in healthy, adenoma, and CRC subjects. BA_E, BL_E, and S_E clusters were dominated by Bacteroide, Blautia, and Streptococcus, respectively. Differences in gut microbial composition were observed within the control, adenoma, CRC populations for each enterotype. S_E showed better performance in distinguishing three human cohorts than BA_E and BL_E. Disease prediction performance of enterotypes is no better than that of a classification model based on all samples.","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":"12 1","pages":""},"PeriodicalIF":4.2,"publicationDate":"2024-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139981686","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TRS-PCR profiles correlate with polymorphisms of the genomic o454-nlpD region, virulence factors repertoire, and phylogenetic groups among uropathogenic Escherichia coli strains isolated from patients from Lodz region, Poland.","authors":"Anna B Kubiak-Szeligowska, Marta Majchrzak, Pawel Parniewski","doi":"10.1186/s13099-024-00603-1","DOIUrl":"10.1186/s13099-024-00603-1","url":null,"abstract":"<p><p>Extraintestinal urinary tract infections are mainly caused by uropathogenic strains of E. coli. UPECs are a heterogeneous group of strains possessing various genes associated with virulence traits. It was demonstrated that changes in the composition of the o454-nlpD region and genetic variation in the mutS-rpoS chromosomal region in ExPEC strains are correlated with their virulence, particularly in those with the pattern III o454-nlpD region and belonging to phylogenetic group B2. In this study, we investigated the presence and distribution of the o454-nlpD genomic polymorphism in our collection of 124 uropathogenic E. coli strains, examining the correlation of o454-nlpD region types with the virulence factors studied. Our findings revealed a positive association between certain virulence factors in UPEC strains and the presence of pattern III in the o454-nlpD region. Additionally, all these strains were classified under phylogenetic group B2. We also showed that the highly pathogenic group of E. coli identified by examining the polymorphism of the o454-nlpD region coincides with the highly pathogenic group of uropathogens we identified in the averaged TRS-PCR analysis.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":"16 1","pages":"11"},"PeriodicalIF":4.2,"publicationDate":"2024-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10885528/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139939936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Timing and clinical risk factors for early acquisition of gut pathogen colonization with multidrug resistant organisms in the intensive care unit","authors":"Loren Shamalov, Madison Heath, Elissa Lynch, Daniel A. Green, Angela Gomez-Simmonds, Daniel E. Freedberg","doi":"10.1186/s13099-024-00605-z","DOIUrl":"https://doi.org/10.1186/s13099-024-00605-z","url":null,"abstract":"Microbiome restitution therapies are being developed to prevent gut pathogen colonization among patients in the intensive care unit (ICU) and in other select populations. If preventive therapies are to be effective, they must be administered prior to pathogen acquisition. The timing and risk factors for early acquisition of gut pathogen colonization (within 72 h) are currently unknown and could be helpful to guide ICU trial design. This was a prospective cohort study. Patients in the ICU had deep rectal swabs performed within 4 h of ICU admission and exactly 72 h later. Early gut pathogen colonization was classified as the new presence (based on culture of rectal swabs) of one or more of the following organisms of interest: methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant (VRE), and Gram-negative bacteria that showed multidrug resistance (MDR) or third generation Cephalosporin resistance (Ceph-R). Clinical risk factors for early acquisition of gut pathogen colonization were captured using the Acute Physiology and Chronic Health Evaluation IV (APACHE IV) scoring system. Among 131 patients who were swabbed at ICU admission and 72 h later, the rates of gut pathogen colonization at ICU admission were 11.4%, 10.6%, 38.6%, and 8.3% for MRSA, VRE, MDR and Ceph-R Gram-negatives respectively. Among the patients who were negative for a given pathogen at ICU admission, the rates of early acquisition of gut pathogen colonization were 7.8% for MRSA (95% CI 3.6 to 14.2%), 7.7% for VRE (95% CI 3.6 to 14.1%), 11.3% for MDR Gram-negatives (95% CI 4.4 to 18.8%), and 4.2% for Ceph-R Gram-negatives (95% CI 1.4 to 9.5%). There were no clinical risk factors which independently predicted early acquisition of gut pathogen colonization. Early gut pathogen colonization was common in the ICU, but our single-center study could not identify any clinical risk factors which were significantly associated with acquisition of gut pathogens.","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":"19 1","pages":""},"PeriodicalIF":4.2,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139922414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"16S rRNA sequencing analysis of the oral and fecal microbiota in colorectal cancer positives versus colorectal cancer negatives in Iranian population.","authors":"Sama Rezasoltani, Mehdi Azizmohammad Looha, Hamid Asadzadeh Aghdaei, Seyedesomayeh Jasemi, Leonardo Antonio Sechi, Maria Gazouli, Amir Sadeghi, Shirin Torkashvand, Reyhaneh Baniali, Hartmut Schlüter, Mohammad Reza Zali, Mohammad Mehdi Feizabadi","doi":"10.1186/s13099-024-00604-0","DOIUrl":"10.1186/s13099-024-00604-0","url":null,"abstract":"<p><strong>Background: </strong>Colorectal cancer (CRC) poses a significant healthcare challenge, accounting for nearly 6.1% of global cancer cases. Early detection, facilitated by population screening utilizing innovative biomarkers, is pivotal for mitigating CRC incidence. This study aims to scrutinize the fecal and salivary microbiomes of CRC-positive individuals (CPs) in comparison to CRC-negative counterparts (CNs) to enhance early CRC diagnosis through microbial biomarkers.</p><p><strong>Material and methods: </strong>A total of 80 oral and stool samples were collected from Taleghani Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran, encompassing both CPs and CNs undergoing screening. Microbial profiling was conducted using 16S rRNA sequencing assays, employing the Nextera XT Index Kit on an Illumina NovaSeq platform.</p><p><strong>Results: </strong>Distinct microbial profiles were observed in saliva and stool samples of CPs, diverging significantly from those of CNs at various taxonomic levels, including phylum, family, and species. Saliva samples from CPs exhibited abundance of Calothrix parietina, Granulicatella adiacens, Rothia dentocariosa, and Rothia mucilaginosa, absent in CNs. Additionally, Lachnospiraceae and Prevotellaceae were markedly higher in CPs' feces, while the Fusobacteria phylum was significantly elevated in CPs' saliva. Conversely, the non-pathogenic bacterium Akkermansia muciniphila exhibited a significant decrease in CPs' fecal samples compared to CNs.</p><p><strong>Conclusion: </strong>Through meticulous selection of saliva and stool microbes based on Mean Decrease GINI values and employing logistic regression for saliva and support vector machine models for stool, we successfully developed a microbiota test with heightened sensitivity and specificity for early CRC detection.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":"16 1","pages":"9"},"PeriodicalIF":4.2,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10880352/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139912485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Intestinal metabolites predict treatment resistance of patients with depression and anxiety.","authors":"Juntaro Matsuzaki, Shunya Kurokawa, Chiaki Iwamoto, Katsuma Miyaho, Akihiro Takamiya, Chiharu Ishii, Akiyoshi Hirayama, Kenji Sanada, Shinji Fukuda, Masaru Mimura, Taishiro Kishimoto, Yoshimasa Saito","doi":"10.1186/s13099-024-00601-3","DOIUrl":"10.1186/s13099-024-00601-3","url":null,"abstract":"<p><strong>Background: </strong>The impact of the gut microbiota on neuropsychiatric disorders has gained much attention in recent years; however, comprehensive data on the relationship between the gut microbiome and its metabolites and resistance to treatment for depression and anxiety is lacking. Here, we investigated intestinal metabolites in patients with depression and anxiety disorders, and their possible roles in treatment resistance.</p><p><strong>Results: </strong>We analyzed fecal metabolites and microbiomes in 34 participants with depression and anxiety disorders. Fecal samples were obtained three times for each participant during the treatment. Propensity score matching led us to analyze data from nine treatment responders and nine non-responders, and the results were validated in the residual sample sets. Using elastic net regression analysis, we identified several metabolites, including N-ε-acetyllysine; baseline levels of the former were low in responders (AUC = 0.86; 95% confidence interval, 0.69-1). In addition, fecal levels of N-ε-acetyllysine were negatively associated with the abundance of Odoribacter. N-ε-acetyllysine levels increased as symptoms improved with treatment.</p><p><strong>Conclusion: </strong>Fecal N-ε-acetyllysine levels before treatment may be a predictive biomarker of treatment-refractory depression and anxiety. Odoribacter may play a role in the homeostasis of intestinal L-lysine levels. More attention should be paid to the importance of L-lysine metabolism in those with depression and anxiety.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":"16 1","pages":"8"},"PeriodicalIF":4.2,"publicationDate":"2024-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10854080/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139711827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A systematic review and meta-analysis of protozoan parasite infections among patients with mental health disorders: an overlooked phenomenon.","authors":"Amir Abdoli, Meysam Olfatifar, Aida Vafae Eslahi, Zeinab Moghadamizad, Rasoul Samimi, Mohammad Amin Habibi, Amir Sam Kianimoghadam, Milad Badri, Panagiotis Karanis","doi":"10.1186/s13099-024-00602-2","DOIUrl":"10.1186/s13099-024-00602-2","url":null,"abstract":"<p><strong>Background: </strong>Patients with mental disorders have a high risk of intestinal parasitic infection due to poor hygiene practices. Hence, to better clarify this overlooked phenomenon, the current study is conducted to determine the global prevalence of protozoan parasite infections in patients with mental disorders and investigate the associated risk factors.</p><p><strong>Methods: </strong>Several databases (PubMed, Scopus, Web of Science, ProQuest, and Google Scholar) were searched for papers published until December 2022. The fixed effect meta-analysis was used to estimate the overall odds ratio (OR) and pooled prevalence was estimated using a random-effects model with a 95% confidence interval (CI).</p><p><strong>Results: </strong>Totally, 131 articles (91 case-control and 40 cross-sectional studies) met the eligibility criteria. Patients with mental disorders were significantly at higher risk for protozoan parasites than healthy controls (OR: 2.059, 1.830-2.317). The highest pooled OR (2.485, 1.413-4.368) was related to patients with neurodevelopmental disorders, and the highest pooled prevalence was detected in patients with neurodevelopmental disorders (0.341, 0.244-0.446), followed by bipolar and related disorders (0.321, 0.000-0.995). Toxoplasma gondii was the most prevalent protozoan parasite (0.343, 0.228-0.467) in cross-sectional studies and the highest pooled OR was related to Cyclospora cayetanensis (4.719, 1.352-16.474) followed by Cryptosporidium parvum (4.618, 2.877-7.412).</p><p><strong>Conclusion: </strong>Our findings demonstrated that individuals afflicted with mental disorders are significantly more susceptible to acquiring protozoan parasites in comparison to healthy individuals. Preventive interventions, regular screening, and treatment approaches for parasitic diseases should be considered for patients with mental disorders.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":"16 1","pages":"7"},"PeriodicalIF":4.3,"publicationDate":"2024-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10822187/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139570411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cyclic-di-AMP confers an invasive phenotype on Escherichia coli through elongation of flagellin filaments.","authors":"Rika Tanaka, Jin Imai, Eiji Sugiyama, Shogo Tsubaki, Katsuto Hozumi, Hitoshi Tsugawa","doi":"10.1186/s13099-024-00600-4","DOIUrl":"10.1186/s13099-024-00600-4","url":null,"abstract":"<p><strong>Background: </strong>Adherent-invasive Escherichia coli (AIEC) is isolated from patients with Crohn's disease (CD). AIEC can invade the intestinal epithelium, suggesting that it is involved in the development and pathogenesis of CD. However, the mechanism by which AIEC acquired the invasive phenotype remains unknown.</p><p><strong>Results: </strong>This study was designed to examine the mechanisms of AIEC invasiveness. We found that the flagellin (fliC) expression in AIEC was two-fold higher than that in non-AIEC strains, and this overexpression induced the formation of long-filament flagellin. Deletion of fliC in the AIEC LF82 strain resulted in the disappearance of flagellar filaments and attenuated the motility and invasive ability of the bacterium, suggesting that the formation of long filament flagellin induced by increased fliC expression is required by AIEC to invade the intestinal epithelium. In AIEC and non-AIEC K12 strains cultured in the presence of cyclic-di-AMP (c-di-AMP), the expression of fliC was enhanced, and flagellar filaments were elongated. Stimulation with c-di-AMP enhanced the bacterial motility and ability to invade epithelial cells, even in the non-AIEC K12 strain.</p><p><strong>Conclusions: </strong>Our findings show that c-di-AMP confers an AIEC-like phenotype on non-AIEC strains by enhancing the expression of fliC. The results should be useful for understanding the pathogenesis of CD.</p>","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":"16 1","pages":"6"},"PeriodicalIF":4.2,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10809763/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139545959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gut microbial ecology and exposome of a healthy Pakistani cohort","authors":"Farzana Gul, Hilde Herrema, Mark Davids, Ciara Keating, Arshan Nasir, Umer Zeeshan Ijaz, Sundus Javed","doi":"10.1186/s13099-024-00596-x","DOIUrl":"https://doi.org/10.1186/s13099-024-00596-x","url":null,"abstract":"Pakistan is a multi-ethnic society where there is a disparity between dietary habits, genetic composition, and environmental exposures. The microbial ecology of healthy Pakistani gut in the context of anthropometric, sociodemographic, and dietary patterns holds interest by virtue of it being one of the most populous countries, and also being a Lower Middle Income Country (LMIC). 16S rRNA profiling of healthy gut microbiome of normo-weight healthy Pakistani individuals from different regions of residence is performed with additional meta-data collected through filled questionnaires. The current health status is then linked to dietary patterns through $${chi }^{2}$$ test of independence and Generalized Linear Latent Variable Model (GLLVM) where distribution of individual microbes is regressed against all recorded sources of variability. To identify the core microbiome signature, a dynamic approach is used that considers into account species occupancy as well as consistency across assumed grouping of samples including organization by gender and province of residence. Fitting neutral modeling then revealed core microbiome that is selected by the environment. A strong determinant of disparity is by province of residence. It is also established that the male microbiome is better adapted to the local niche than the female microbiome, and that there is microbial taxonomic and functional diversity in different ethnicities, dietary patterns and lifestyle habits. Some microbial genera, such as, Megamonas, Porphyromonas, Haemophilus, Klebsiella and Finegoldia showed significant associations with consumption of pickle, fresh fruits, rice, and cheese. Our analyses suggest current health status being associated with the diet, sleeping patterns, employment status, and the medical history. This study provides a snapshot of the healthy core Pakistani gut microbiome by focusing on the most populous provinces and ethnic groups residing in predominantly urban areas. The study serves a reference dataset for exploring variations in disease status and designing personalized dietary and lifestyle interventions to promote gut health, particularly in LMICs settings.","PeriodicalId":12833,"journal":{"name":"Gut Pathogens","volume":"3 1","pages":""},"PeriodicalIF":4.2,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139515083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}