16S rRNA Sequencing Reveals Alterations of Gut Bacteria in Hirschsprung-Associated Enterocolitis
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ABSTRACT:
SUBMITTER: Shi H
PROVIDER: S-EPMC11341197 | biostudies-literature | 2024 Aug
REPOSITORIES: biostudies-literature
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Project description:Nonalcoholic fatty liver disease (NAFLD) is a prevalent and progressive disease spectrum ranging from nonalcoholic fatty liver (NAFL) to nonalcoholic steatohepatitis (NASH), yet there is no effective treatment and efficient noninvasive diagnostic method for NASH. The present study investigated the longitudinal alternations of gut microbiota in the Western diet (WD) induced murine NAFLD model using 16S rRNA sequencing. Evident steatosis and inflammation were detected in the liver at the 8th and 12th week, while prompted hepatic oxidative injury and fibrosis were found at the 16th week. In this progressive process, impaired bile acid (BA) metabolism plays a vital part. Long-term WD intervention alters microbial richness and composition in the intestine, shaping characteristic microbial feature correspondence to each NAFLD stage. Descending abundances of Clostridia and Ruminococcaceae were found in NAFLD progression, while inflammation-related microbes [Eubacterium]_fissicatena_group, Romboutsia, and Erysipelatoclostridium were verified to identify borderline NASH at 8th and 12th week, and BA-associated taxa Dubosiella, Bosea, Helicobacter, and Alistipes were recognized as special symbols reflecting the state of oxidative damage and fibrosis in NASH at 16th week. Further, feces and colon abundances of Akkermansia were verified to be depleted in the process of borderline NASH progressed to NASH, and exhibited substantial correlations with NAFLD indexes ALT, AST, TC, and TBA. These characteristic taxa were effective to identify NAFLD and NASH, and microbiota-derived predictive models for NAFLD and NASH exhibited great potential (AUC 0.983 and 0.784). These findings demonstrate that a core set of gut microbiome especially BA-related taxa may be adopted as a noninvasive diagnostic tool for NAFLD and NASH. IMPORTANCE This study concentrates on longitudinal alternations of gut microbiota in NAFLD progression and discovers the interrelationships between them. These findings may uncover the role of gut microbiota in NAFLD progression and identify novel noninvasive diagnostic tools for NAFLD based on microbial biomarkers.
| S-EPMC9241867 | biostudies-literature
Project description:Insects have a long history of being used in medicine, with clear primary and secondary functions and less side effects, and the study and exploitation of medicinal insects have received increasing attention. Insects gut microbiota and their metabolites play an important role in protecting the hosts from other potentially harmful microbes, providing nutrients, promoting digestion and degradation, and regulating growth and metabolism of the hosts. However, there are still few studies linking the medicinal values of insects with their gut microbes. In this study, we focused on the specific gut microbiota common to medicinal insects, hoping to trace the potential connection between medicinal values and gut microbes of medicinal insects. Based on 16S rRNA gene sequencing data, we compared the gut microbiota of medicinal insects [Periplaneta americana, Protaetia (Liocola) brevitarsis (Lewis) and Musca domestica], in their medicinal stages, and non-medicinal insects (Hermetia illucens L., Tenebrio molitor, and Drosophila melanogaster), and found that the intestinal microbial richness of medicinal insects was higher, and there were significant differences in the microbial community structure between the two groups. We established a model using a random-forest method to preliminarily screen out several types of gut microbiota common to medicinal insects that may play medicinal values: Parabacteroides goldsteinii, Lactobacillus dextrinicus, Bifidobacterium longum subsp. infantis (B. infantis), and Vagococcus carniphilus. In particular, P. goldsteinii and B. infantis were most probably involved in the anti-inflammatory effects of medicinal insects. Our results revealed an association between medicinal insects and their gut microbes, providing new development directions and possibly potential tools for utilizing microbes to enhance the medicinal efficacy of medicinal insects.
| S-EPMC9149300 | biostudies-literature
Project description:BackgroundBiliary atresia (BA) is a severe neonatal disease with progressive intra- and extra-hepatic bile ducts inflammation and hepatic fibrosis. Characterization of gut microbiome profiles in infants with biliary atresia can provide valuable information and potential disease biomarkers. Our study aims to explore the relationship between gut microbiota and biliary atresia.Methods16 S ribosomal RNA (rRNA) gene sequencing was carried out to identify the differences in composition and diversity of gut microbiota between infants with BA and healthy subjects. A total of 31 infants with biliary atresia and 20 healthy subjects were recruited.ResultsThe composition of gut microbiota in BA group was significantly different with the normal control group (P < 0.05) and the abundance ratio of Klebsiella/Bifidobacterium showed great potential for identification of BA (P < 0.01). In addition, the differential bacterial taxa were involved in lipid and vitamins metabolism.ConclusionOur results could provide potential non-invasive biomarker for identification of biliary atresia and contribute to the treatment in terms of ameliorating microbiota dysbiosis.
| S-EPMC10865691 | biostudies-literature
Project description:Recently, there has been a rapid increase in studies on the relationship between brain diseases and gut microbiota, and clinical evidence on gut microbial changes in Parkinson's disease (PD) has accumulated. 6-Hydroxydopamine (6-OHDA) is a widely used neurotoxin that leads to PD pathogenesis, but whether 6-OHDA affects gut microbial environment has not been investigated. Here we performed the 16S rRNA gene sequencing to analyze the gut microbial community of mice. We found that there were no significant changes in species richness and its diversity in the 6-OHDA-lesioned mice. The relative abundance of Lactobacillus gasseri and L. reuteri probiotic species in feces of 6-OHDA-lesioned mice was significantly decreased compared with those of sham-operated mice, while the commensal bacterium Bacteroides acidifaciens in 6-OHDA-treated mice was remarkably higher than sham-operated mice. These results provide a baseline for understanding the microbial communities of 6-OHDA-induced PD model to investigate the role of gut microbiota in the pathogenesis of PD.
| S-EPMC6690581 | biostudies-literature
Project description:BackgroundObesity is a global epidemic in the industrialized and developing world, and many children suffer from obesity-related complications. Gut microbiota dysbiosis might have significant effect on the development of obesity. The microbiota continues to develop through childhood and thus childhood may be the prime time for microbiota interventions to realize health promotion or disease prevention. Therefore, it is crucial to understand the structure and function of pediatric gut microbiota.MethodsAccording to the inclusion criteria and exclusion criteria, twenty-three normal weight and twenty-eight obese children were recruited from Nanjing, China. Genomic DNA was extracted from fecal samples. The V4 region of the bacterial 16S rDNA was amplified by PCR, and sequencing was applied to analyze the gut microbiota diversity and composition using the Illumina HiSeq 2500 platform.ResultsThe number of operational taxonomic units (OTUs) showed a decrease in the diversity of gut microbiota with increasing body weight. The alpha diversity indices showed that the normal weight group had higher abundance and observed species than the obese group (Chao1: P < 0.001; observed species: P < 0.001; PD whole tree: P < 0.001; Shannon index: P = 0.008). Principal coordinate analysis (PCoA) and Nonmetric multidimensional scaling (NMDS) revealed significant differences in gut microbial community structure between the normal weight group and the obese group. The liner discriminant analysis (LDA) effect size (LEfSe) analysis showed that fifty-five species of bacteria were abundant in the fecal samples of the normal weight group and forty-five species of bacteria were abundant in the obese group. In regard to phyla, the gut microbiota in the obese group had lower proportions of Bacteroidetes (51.35%) compared to the normal weight group (55.48%) (P = 0.030). There was no statistical difference in Firmicutes between the two groups (P = 0.436), and the Firmicutes/Bacteroidetes between the two groups had no statistical difference (P = 0.983). At the genus level, Faecalibacterium, Phascolarctobacterium, Lachnospira, Megamonas, and Haemophilus were significantly more abundant in the obese group than in the normal weight group (P = 0.048, P = 0.018, P < 0.001, P = 0.040, and P = 0.003, respectively). The fecal microbiota of children in the obese group had lower proportions of Oscillospira and Dialister compared to the normal weight group (P = 0.002 and P = 0.002, respectively).ConclusionsOur results showed a decrease in gut microbiota abundance and diversity as the BMI increased. Variations in the bacterial community structure were associated with obesity. Gut microbiota dysbiosis might play a crucial part in the development of obesity in Chinese children.
| S-EPMC6968493 | biostudies-literature
Project description:BackgroundPsoriasis is an inflammatory skin disease. The correlation between intestinal microbiota and immune-mediated diseases makes scientists pay attention to the pathogenic role of microbiota.ObjectiveThe aim of this study was to identify the gut microbial composition of patients with psoriasis.Methods16S rRNA gene sequencing method was used to analyse the faecal samples which was collected from 28 moderately severe psoriasis patients and 21 healthy controls and was followed by the analysing of informatics methods.ResultsNo visible differences can be observed in the diversity of gut microbiota between the psoriasis and the healthy patients, but the composition of the gut microbiota illustrate significant distinction between these two groups. At the phylum level, compared to the healthy control group, the psoriasis group shows higher relative abundance of Bacteroidetes and lower relative abundance of Proteobacteria (P < 0.05). At the genus level, unidentified_Enterobacteriaceae, unidentified_Lachnospiraceae, Romboutsia, Subdoligranulum, unidentified_Erysipelotrichaceae, Dorea were relatively less abundant in psoriasis patients, whereas Lactobacillus, Dialister were relatively more abundant in psoriasis group (all P < 0.05). LefSe analysis (linear discriminant analysis effect size) indicated that Negativicutes and Bacteroidia were potential biomarkers for psoriasis.ConclusionThis study identified the intestinal microecological environment of patients with psoriasis and healthy people, proving that psoriasis patients have a remarkably disturbed microbiome, and found several biomarkers of intestinal microorganisms in patients with psoriasis.
| S-EPMC9971763 | biostudies-literature
Project description:Renal stones are a common urological disease with high prevalence and recurrence rates. Characterizing gut microbiome profiles of first-onset renal calculi patients, both before and after surgery, may provide valuable insights and identify potential biomarkers for the disease. In this study, we explored the associations between the gut microbiome and renal stone formation using 16S ribosomal RNA (rRNA) gene sequencing. In brief, 20 patients were recruited, and information on health and eating habits within the previous 1-3 months was collected upon admission. A total of 493 operational taxonomic units (OTUs) were detected in 40 specimens, with an average of 67,888 ± 827 reads per sample. The results of OTU-based partial least squares discriminant analysis (PLS-DA) analysis showed differences between RS1 (fecal specimen before surgery) and RS2 (one month later after surgery) groups, with a significantly higher level of OTU7 in the RS2 group. Taxonomy-based comparisons of the gut microbiome showed differences in the flora composition, with the prevalence of Enterobacteriales, Enterobacteriaceae, Gammaproteobacteria and Escherichia being higher in the RS2 group and the prevalence of Pseudomonadaceae, Pseudomonadales and Pseudomonas being higher in the RS1 group. Correlation analysis showed that an increased prevalence of Enterobacteriaceae, Gammaproteobacteria and Escherichia associated with a decreased level of urea, and a decreased creatinine level was correlated with an increased prevalence of Escherichia. These data strongly suggest that the gut microbiome plays an important role in kidney stone formation, and these findings may provide new insights for the prevention, diagnosis, and treatment of renal stones.
| S-EPMC9544399 | biostudies-literature
Project description:BackgroundThe gut microbiota plays a crucial role in metabolic dysfunction-associated steatotic liver disease (MASLD). Next-generation sequencing technologies are essential for exploring the gut microbiome. While recent advancements in full-length 16S (FL16S) rRNA sequencing offer better taxonomic resolution, whether they establish stronger associations with the risk of MASLD remains to be determined.MethodThis study utilized long-read FL16S and short-read V3-V4 16S rRNA sequencing to profile gut microbiome compositions in age-, sex-, and BMI-matched case-control pairs of obese children with and without MASLD. A random forest predictive model was employed, using gut-microbiota features selected based on the top 35 most abundant taxa or a linear discriminant analysis score greater than 3. The model's performance was evaluated by comparing the area under the receiver operating characteristic curve (AUC) through a tenfold cross-validation method.ResultsSubjects with MASLD exhibited significantly elevated serum alanine aminotransferase, triglycerides, and homeostasis model assessment of insulin resistance levels compared to controls. At the genus level, the gut microbiome compositions detected by both FL16S and V3-V4 sequencing were similar, predominantly comprising Phocaeicola and Bacteroides, followed by Prevotella, Bifidobacterium, Parabacteroides, and Blautia. The AUC for the model based on FL16S sequencing data (86.98%) was significantly higher than that based on V3-V4 sequencing data (70.27%), as determined by DeLong's test (p = 0.008).ConclusionFL16S rRNA sequencing data demonstrates stronger associations with the risk of MASLD in obese children, highlighting its potential for real-world clinical applications.
| S-EPMC11912586 | biostudies-literature
Project description:The human impact on natural habitats is increasing the complexity of human-wildlife interactions and leading to the emergence of infectious diseases worldwide. Highly successful synanthropic wildlife species, such as rodents, will undoubtedly play an increasingly important role in transmitting zoonotic diseases. We investigated the potential for recent developments in 16S rRNA amplicon sequencing to facilitate the multiplexing of the large numbers of samples needed to improve our understanding of the risk of zoonotic disease transmission posed by urban rodents in West Africa. In addition to listing pathogenic bacteria in wild populations, as in other high-throughput sequencing (HTS) studies, our approach can estimate essential parameters for studies of zoonotic risk, such as prevalence and patterns of coinfection within individual hosts. However, the estimation of these parameters requires cleaning of the raw data to mitigate the biases generated by HTS methods. We present here an extensive review of these biases and of their consequences, and we propose a comprehensive trimming strategy for managing these biases. We demonstrated the application of this strategy using 711 commensal rodents, including 208 Mus musculus domesticus, 189 Rattus rattus, 93 Mastomys natalensis, and 221 Mastomys erythroleucus, collected from 24 villages in Senegal. Seven major genera of pathogenic bacteria were detected in their spleens: Borrelia, Bartonella, Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia. Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia have never before been detected in West African rodents. Bacterial prevalence ranged from 0% to 90% of individuals per site, depending on the bacterial taxon, rodent species, and site considered, and 26% of rodents displayed coinfection. The 16S rRNA amplicon sequencing strategy presented here has the advantage over other molecular surveillance tools of dealing with a large spectrum of bacterial pathogens without requiring assumptions about their presence in the samples. This approach is therefore particularly suitable to continuous pathogen surveillance in the context of disease-monitoring programs. IMPORTANCE Several recent public health crises have shown that the surveillance of zoonotic agents in wildlife is important to prevent pandemic risks. High-throughput sequencing (HTS) technologies are potentially useful for this surveillance, but rigorous experimental processes are required for the use of these effective tools in such epidemiological contexts. In particular, HTS introduces biases into the raw data set that might lead to incorrect interpretations. We describe here a procedure for cleaning data before estimating reliable biological parameters, such as positivity, prevalence, and coinfection, using 16S rRNA amplicon sequencing on an Illumina MiSeq platform. This procedure, applied to 711 rodents collected in West Africa, detected several zoonotic bacterial species, including some at high prevalence, despite their never before having been reported for West Africa. In the future, this approach could be adapted for the monitoring of other microbes such as protists, fungi, and even viruses.
| S-EPMC5069956 | biostudies-literature
Project description:The gut and brain interact through various metabolic and signaling pathways, each of which influences mental health. Gut dysbiosis caused by antibiotics is a well-known phenomenon that has serious implications for gut microbiota-brain interactions. Although antibiotics disrupt the gut microbiota's fundamental structure, the mechanisms that modulate the response and their impact on brain function are still unclear. It is imperative to comprehend and investigate crucial regulators and factors that play important roles. We aimed to study the effect of long-term antibiotic-induced disruption of gut microbiota, host metabolomes, and brain function and, particularly, to determine the basic interactions between them by treating the C57BL/6 mice with two different, most commonly used antibiotics, ciprofloxacin and amoxicillin. Anxiety-like behavior was confirmed by the elevated plus-maze test and open field test. Gut microbes and their metabolite profiles in fecal, serum, and brain samples were determined by 16S rRNA sequencing and untargeted metabolomics. In our study, long-term antibiotic treatment exerted anxiety-like effects. The fecal microbiota and metabolite status revealed that the top five genera found were Lactobacillus, Bacteroides, Akkermansia, Ruminococcus_gnavus_group, and unclassified norank_f_Muribaculaceae. The concentration of serotonin, L-Tyrosine, 5-Hydroxy-L-tryptophan, L-Glutamic acid, L-Glutamate, 5-Hydroxyindole acetic acid, and dopaminergic synapsis was comparatively low, while adenosine was high in antibiotic-treated mice. The KEGG enrichment analysis of serum and brain samples showed that amino acid metabolism pathways, such as tryptophan metabolism, threonine metabolism, serotonergic synapsis, methionine metabolism, and neuroactive ligand-receptor interaction, were significantly decreased in antibiotic-treated mice. Our study demonstrates that long-term antibiotic use induces gut dysbiosis and alters metabolic responses, leading to the dysregulation of brain signaling molecules and anxiety-like behavior. These findings highlight the complex interactions between gut microbiota and metabolic functions, providing new insights into the influence of microbial communities on gut-brain communication.
| S-EPMC11906700 | biostudies-literature