Fecal Samples Of Patients Research Articles

Chlorella modulation of gut microbiota dysbiosis in patients with type-2 diabetes

To investigate the effects of Chlorella alga on gut microbiota dysbiosis in type-2 diabetes (T2D). The stress perception of patients was also investigated. Chlorella (3 g/day) was administered to patients with T2D (n = 10) for a period of 30 days. Gut microbiota composition was analysed by 16S rDNA gene sequencing, and stress perception was evaluated using the perceived stress scale (PSS). A total of 13 phyla, 89 families, and 185 genera were identified from all faecal samples of patients with T2D, and Firmicutes and Bacteroidetes were the most dominant phyla among all samples. Chlorella decreased Bacteroidetes and increased Firmicutes. The proportions of the Akkermansia, Coprococcus, Dorea, Lachnospira, Phascolarctobacterium, and Ruminococcus generas increased, whereas the proportion of Paraprevotella, Prevotella, Klebsiella, and Sutterella decreased in the faeces of patients with T2D after Chlorella intake. Chlorella induced a significant reduction in perceived stress in patients with T2D, and better PSS scores negatively correlated with an increase in Akkermansia, Coprococcus, Dorea, Lachnospira, Phascolarctobacterium, and Ruminococcus and positively correlated with a decrease in Paraprevotella, Prevotella, Klebsiella, and Sutterella. Altogether, these results show the ability of Chlorella to positively modulate gut dysbiosis, leading to reduced stress perception in patients with T2D. Our findings contribute to the globally increasing search for new preventive and therapeutic strategies aimed at restoring the balance of the intestinal ecosystem.

Short-chain fatty acids in faecal samples of patients with schizophrenia and bipolar disorder: are there differences based on the diagnosis?

Short-chain fatty acids in faecal samples of patients with schizophrenia and bipolar disorder: are there differences based on the diagnosis?

How is gut microbiome of patients with familial adenomatous polyposis different from healthy people?

The gut microbiome has been increasingly suggested as an underlying cause of various human diseases. In this study, we hypothesized that the gut microbiomes of patients with familial adenomatous polyposis (FAP) are different from those of healthy people and attempted to identify the associations between gut microbiome characteristics and FAP. We collected fecal samples from patients with FAP and healthy volunteers and evaluated the diversity, composition, and distribution of the gut microbiome between the 2 groups via 16S rRNA-based taxonomic profiling of the fecal samples. Fecal samples were collected from 10 patients with FAP (4 men and 6 women, mean age 39.2 ± 13.8 years) and 10 healthy volunteers (4 men and 6 women, mean age 40.9 ± 9.8 years). The microbial richness in patients with FAP was significantly lower than that in healthy people. Regarding microbial composition, the Firmicutes/Bacteroidetes ratio in patients with FAP was higher than that in healthy people, especially in those with a lower proportion of Bacteroidetes and a higher proportion of Proteobacteria. We also found 7 specific abundant strains in fecal samples of patients with FAP. Patients with FAP had different Firmicutes/Bacteroidetes ratios and Proteobacteria abundance compared to healthy people and showed the presence of specific bacteria. These findings suggest a promising role of the gut microbiome in patients with FAP, although further studies are needed.

Gut bacteriome and metabolome of Ascaris lumbricoides in patients

The most frequent intestinal helminth infections in humans are attributed to Ascaris lumbricoides, and there are concerns over the anthelminthic resistance of this species. The gut microbiota has essential roles in host physiology. Therefore, discovering host-parasite–microbiota interactions could help develop alternative helminthiasis treatments. Additionally, these interactions are modulated by functional metabolites that can reveal the mechanisms of infection and disease progression. Thus, we aimed to investigate bacteriomes in the gut of helminths and fecal samples of patients via next-generation sequencing. Our results showed that infection intensity was associated with the bacterial composition of helminth guts but not with the intestinal bacteriome of human hosts. Moreover, the metabolomes of A. lumbricoides in the heavy and light ascariasis cases were characterized using ultra-high performance liquid chromatography/time-of-flight mass spectrometry. Increased levels of essential biomolecules, such as amino acids, lipids, and nucleotide precursors, were found in the guts of helminths isolated from heavily infected patients, implying that these metabolites are related to egg production and ascariasis pathogenicity. These findings are the first step towards a more complete understanding of the mechanisms by which the bacteriome of helminth guts affect their colonization and may reveal novel and more effective approaches to parasitic disease therapy.

Uncovering the characteristics of the gut microbiota in patients with acute ischemic stroke and phlegm-heat syndrome.

Growing evidence has indicated that the characteristics of gut microbiota are associated with acute ischemic stroke (AIS). Phlegm-heat syndrome (PHS), a specific pathological state of the AIS, is one of the common traditional Chinese syndromes of stroke. The long duration of PHS in patients with AIS could lead to poor clinical outcomes. Gut microbiota characteristics in patients with both AIS and PHS, and their relationship remains unknown. This study was designed to investigate the alterations in gut microbiota in patients with AIS and PHS through a cross-sectional study. Fecal samples were collected from 10 patients with AIS and non-PHS (ntAIS), 7 patients with AIS and PHS (tAIS), and 10 healthy controls (HC). Samples were profiled via Illumina sequencing of the 16S rRNA V3-V4. Stroke severity was assessed at admission by the National Institutes of Health Stroke Scale (NIHSS) and modified Rankin scale (mRS); their correlation with gut microbiota was investigated. The alpha-diversity of the bacterial communities was significantly higher in the fecal samples of patients with tAIS than in patients with ntAIS (Shannon index, P = 0.037). In addition, the combined tAIS and ntAIS group (tntAIS) exhibited higher microbiotic diversity when compared with HC (chao1, P = 0.019). The structure of intestinal microbiota was effectively distinguished between the tAIS and ntAIS group (ANOSIM, r = 0.337, P = 0.007). Additionally, the gut microbiota structure was significantly different between the tntAIS and HC groups (ANOSIM, r = 0.217, P = 0.005). The genera, Ruminococcaceae_ UCG_002 and Christensenellaceae_R-7_group, were implicated in the discrimination of PHS from non-PHS. The order Lactobacillales and family Lachnospiraceae were significantly negatively correlated with NIHSS and mRS at admission (P < 0.05). By contrast, the order Desulfovibrionales, families Christensenellaceae and Desulfovibrionaceae, and genera Ruminococcaceae UCG-014 and Ruminococcaceae UCG-002 were significantly positively correlated with NIHSS and mRS at admission (P < 0.05). This study is the first to profile the characteristics of gut microbiota in patients with AIS and PHS, compared with those with non-PHS. The genera, Ruminococcaceae_ UCG_002 and Christensenellaceae_R-7_group, may be objective indicators of this traditional Chinese medicine (TCM) syndrome in AIS. Furthermore, it provides a microbe-inspired biological basis for TCM syndrome differentiation.

Altered gut microbiome diversity and function in patients with propionic acidemia.

Propionic acidemia (PA) is an inherited metabolic disorder of propionate metabolism, where the gut microbiota may play a role in pathophysiology and therefore, represent a relevant therapeutic target. Little is known about the gut microbiota composition and activity in patients with PA. Although clinical practice varies between metabolic treatment centers, management of PA requires combined dietary and pharmaceutical treatments, both known to affect the gut microbiota. This study aimed to characterize the gut microbiota and its metabolites in fecal samples of patients with PA compared with healthy controls from the same household. Eight patients (aged 3-14y) and 8 controls (4-31y) were recruited from Center 1 (UK) and 7 patients (11-33y) and 6 controls (15-54y) from Center 2 (Austria). Stool samples were collected 4 times over 3 months, alongside data on dietary intakes and medication usage. Several microbial taxa differed between patients with PA and controls, particularly for Center 1, e.g., Proteobacteria levels were increased, whereas butyrate-producing genera, such as Roseburia and Faecalibacterium, were decreased. Most measured microbial metabolites were lower in patients with PA, and butyrate was particularly depleted in patients from Center 1. Furthermore, microbiota profile of these patients showed the lowest compositional and functional diversity, and lowest stability over 3 months. As the first study to map the gut microbiota of patients with PA, this work represents an important step forward for developing new therapeutic strategies to further improve PA clinical status. New dietary strategies should consider microbial propionate production as well as butyrate production and microbiota stability.

S551 Loss of Bifidobacteria in Lyme Disease: Cause or Effect

Introduction: Lyme disease is a poorly understood condition which starts with a rash but may continue with chronic fatigue and neurological symptoms. Approximately 1 in 5 early Lyme disease patients have GI symptoms, such as nausea, anorexia, abdominal pain, or diarrhea. Lyme disease is thought to be cased by microbes in the spirochetes phylum transmitted by black legged ticks. Lyme-related healthcare costs in America exceed 1.3 billion dollars annually. Bifidobacteria are known for their beneficial probiotic actions within the human gut microbiome. Their numbers are reduced in severe COVID-19, Clostridioides difficile infection and Inflammatory Bowel Disease. To our knowledge Bifidobacteria levels have not been studied in Lyme disease patients. Given the importance of Bifidobacterium abundance in other diseases, we focused on relative abundance of Bifidobacterium in fecal samples of patients with Lyme disease compared to controls. Methods: Fecal samples were assessed for relative abundance of Bifidobacterium in Healthy Control subjects without Lyme disease (n=20) compared to patients with Lyme disease (n=39). The average symptom duration in patients with Lyme disease was 5 years and none were on antibiotics 2 weeks prior to sample collection (range of symptoms from 1 month to 20 years, all treated initially with antibiotics).Metagenomics Next Generation sequencing was performed on fecal samples, where DNA samples were extracted and normalized for library downstream analysis using Shotgun Methodology. Mann-Whitney Statistical test was used for comparison. This study was IRB approved. Results: Relative Abundance of bifidobacteria was significantly decreased (p< 0.0001) in patients with Lyme disease. Median and interquartile range (IQR) were: Control (Median:4.175%; IQR:1.72-10.27%) and Lyme disease (Median:0.0014%; IQR:0.00%-0.96%)(Figure). 30/39 Lyme disease patients (77%) were found to possess < 1% relative abundance of Bifidobacterium in their stool sample. Of interest only 1/39 samples showed presence of Spirochetes in stool samples. Conclusion: This is the first study that demonstrates low levels of Bifidobacteria in patients with chronic Lyme disease. These results raise three questions; whether the disease was caused by 1. the original microbe creating loss of Bifidobacterium 2. baseline low Bifidobacteria due likely to either diet or medications or 3. excessive treatment. Given Lyme disease comprises a gut dysbiosis issue, therapies should also aim at restoration of depleted Bifidobacteria.Figure 1.: Lyme disease subjects have significantly (p<0.001) reduced relative abundance of genus bifidobacterium.

Phylogrouping and characterization of Escherichia coli isolated from colonic biopsies and fecal samples of patients with flare of inflammatory bowel disease in Iran.

BackgroundAlthough the etiopathogenesis of inflammatory bowel disease (IBD) is still poorly understood, Escherichia coli has been described as a potential causative microorganism in IBD pathogenesis and also disease progression, offering a potential therapeutic target for disease management. Therefore, we conducted this study to investigate the pathotypes, phylogenetic groups, and antimicrobial resistance of E. coli isolates from patients with IBD in Iran.MethodsFecal and biopsy colonic samples were collected from IBD patients experiencing flare-up episodes referred to Taleghani hospital in Tehran, Iran, between August 2020 and January 2021. Identification of E. coli strains was performed based on biochemical and molecular methods. Antibiotic susceptibility testing was performed as recommended by the Clinical and Laboratory Standards Institute. Phylogrouping and pathotyping of each isolate were carried out using polymerase chain reaction (PCR) and multilocus sequence typing (MLST) assays.ResultsA total of 132 non-duplicate E. coli strains were isolated from 113 IBD patients, including 96 ulcerative colitis (UC), and 17 Crohn’s disease (CD) patients. In our study, 55% of CD-related E. coli and 70.5% of UC-related isolates were non-susceptible to at least three or more unique antimicrobial classes, and were considered as multidrug-resistant (MDR) strains. E. coli strains exhibited a high level of resistance to cefazolin, ampicillin, tetracycline, ceftazidime, ciprofloxacin, and cefotaxime. Enterotoxigenic E. coli (ETEC) and diffusely adherent E. coli (DAEC) were the most prevalent pathotypes, and groups B2 and D were the predominant phylogroups.ConclusionIn the present study, we found that E. coli strains that colonize the gut of Iranian patients with IBD most frequently belonged to phylogenetic groups B2 and D. We also conclude that E. coli isolates from IBD patients have been revealed to be resistant to commonly used antibiotics, in which most of them harbored strains that would be categorized as MDR.

Clostridium butyricum Protects Against Pancreatic and Intestinal Injury After Severe Acute Pancreatitis via Downregulation of MMP9.

Background: Evidence have shown that gut microbiota plays an important role in the development of severe acute pancreatitis (SAP). In addition, matrix metalloproteinase-9 (MMP9) plays an important role in intestinal injury in SAP. Thus, we aimed to determine whether gut microbiota could regulate the intestinal injury during SAP via modulating MMP9. Methods: In this study, the fecal samples of patients with SAP (n = 72) and healthy controls (n = 32) were analyzed by 16S rRNA gene sequencing. In addition, to investigate the association between gut microbiota and MMP9 in intestinal injury during SAP, we established MMP9 stable knockdown Caco2 and HT29 cells in vitro and generated a MMP9 knockout (MMP9−/−) mouse model of SAP in vivo. Results: We found that the abundance of Clostridium butyricum (C. butyricum) was significantly decreased in the SAP group. In addition, overexpression of MMP9 notably downregulated the expressions of tight junction proteins and upregulated the expressions of p-p38 and p-ERK in Caco2 and HT29 cells (p < 0.05). However, C. butyricum or butyrate treatment remarkably upregulated the expressions of tight junction proteins and downregulated the expressions of MMP9, p-p38 and p-ERK in MMP9-overexpressed Caco2 and HT29 cells (p < 0.05). Importantly, C. butyricum or butyrate could not affect the expressions of tight junction proteins, and MMP9, p-p38 and p-ERK proteins in MMP9-knockdown cells compared with MMP9-knockdown group. Consistently, C. butyricum or butyrate could not attenuate pancreatic and intestinal injury during SAP in MMP9−/− mice compared with the SAP group. Conclusion: Collectively, C. butyricum could protect against pancreatic and intestinal injury after SAP via downregulation of MMP9 in vitro and in vivo.

Probiotic-derived nanoparticles inhibit ALD through intestinal miR194 suppression and subsequent FXR activation.

Intestinal farnesoid X receptor (FXR) plays a critical role in alcohol-associated liver disease (ALD). We aimed to investigate whether alcohol-induced dysbiosis increased intestinal microRNA194 (miR194) that suppressed Fxr transcription and whether Lactobacillus rhamnosus GG-derived exosome-like nanoparticles (LDNPs) protected against ALD through regulation of intestinal miR194-FXR signaling in mice. Binge-on-chronic alcohol exposure mouse model was utilized. In addition to the decreased ligand-mediated FXR activation, alcohol feeding repressed intestinal Fxr transcription and increased miR194 expression. This transcriptional suppression of Fxr by miR194 was confirmed in intestinal epithelial Caco-2 cells and mouse enteriods. The alcohol feeding-reduced intestinal FXR activation was further demonstrated by the reduced FXR reporter activity in fecal samples and by the decreased fibroblast growth factor 15 (Fgf15) messenger RNA (mRNA) in intestine and protein levels in the serum, which caused an increased hepatic bile acid synthesis and lipogeneses. We further demonstrated that alcohol feeding increased-miR194 expression was mediated by taurine-upregulated gene 1 (Tug1) through gut microbiota regulation of taurine metabolism. Importantly, 3-day oral administration of LDNPs increased bile salt hydrolase (BSH)-harboring bacteria that decreased conjugated bile acids and increased gut taurine concentration, which upregulated Tug1, leading to a suppression of intestinal miR194 expression and recovery of FXR activation. Activated FXR upregulated FGF15 signaling and subsequently reduced hepatic bile acid synthesis and lipogenesis and attenuated ALD. These protective effects of LDNPs were eliminated in intestinal FxrΔIEC and Fgf15-/- mice. We further showed that miR194 was upregulated, whereas BSH activity and taurine levels were decreased in fecal samples of patients with ALD. Our results demonstrated that gut microbiota-mediated miR194 regulation contributes to ALD pathogenesis and to the protective effects of LDNPs through modulating intestinal FXR signaling.

Gut microbiota diversity in middle-aged and elderly patients with end-stage diabetic kidney disease.

BackgroundDiabetic kidney disease (DKD) is the most common cause of end-stage renal disease (ESRD), but the mechanism between DKD and ESRD remains unclear. Some experts have put forward the “microbial-centered ESRD development theory”, believing that the bacterial load caused by gut microecological imbalance and uremia toxin transfer are the core pathogenic links. The purpose of this study was to analyze the genomic characteristics of gut microbiota in patients with ESRD, specifically DKD or non-diabetic kidney disease (NDKD).MethodsIn this cross-sectional study, patients with ESRD were recruited in a community, including 22 DKD patients and 22 NDKD patients matched using gender and age. Fecal samples of patients were collected for 16S rDNA sequencing and gut microbiota analysis. The distribution structure, diversity, and abundance of microflora in DKD patients were analyzed by constructing species evolutionary trees and analyzing alpha diversity, beta diversity, and linear discriminant analysis effect size (LEfSe).ResultsThe results of our study showed that there were statistically significant differences in the richness and species of gut microbiota at the total level between DKD patients and NDKD patients. The analysis of genus level between the two groups showed significant differences in 16 bacterial genera. Among them, Oscillibacter, Bilophila, UBA1819, Ruminococcaceae UCG-004, Anaerotruncus, Ruminococcaceae, and Ruminococcaceae NK4A214 bacteria in DKD patients were higher than those in NDKD patients.Conclusions16S rDNA sequencing technology was used in this study to analyze the characteristics of intestinal flora in ESRD patients with or without diabetes. We found that there was a significant difference in the intestinal flora of ESRD patients caused by DKD and NDKD, suggesting that these may be potential causative bacteria for the development of ERSD in DKD patients.

Detecting of beta-lactamase genes in clinical isolates of Escherichia coli isolated from Baqiyatallah Hospital of Bashagard and evaluating their antibiotic resistance and biofilm formation

Biofilm formation has been observed in different species of bacteria such as Escherichia coli and Pseudomonas aeruginosa. The formation of biofilms in the airways of pneumonia patients and chronic lung patients is one of the important factors in prolonging the treatment period, exacerbating clinical symptoms and even death of patients. The present study aimed to investigate beta-lactamase genes in clinical isolates of Escherichia coli isolated from Baqiyatallah Bashagard Hospital and to evaluate their antibiotic resistance and biofilm formation. In the present study, 60 isolates from fecal samples of patients with symptoms of diarrhea and suspected Escherichia coli infection were collected and selected from Baqiyatallah Hospital of Bashagard. After confirmation of Escherichia coli strains using microbial culture and biochemical tests, the presence of three beta-lactamase genes in these isolates was examined. The ability of isolates to form biofilms and their resistance to two different antibiotics were also measured. A phenotypic study of isolates based on optical absorbance measurements showed that among the clinical Escherichia coli isolated from Baqiyatallah Hospital of Bashagard, only 10 isolates could form a strong biofilm in the microtiter plate.

Partial sequence conservation of SARS-CoV-2 NSP-2, NSP-12, and Spike in stool samples from Abadan, Iran.

Since the onset of the coronavirus disease 2019 (COVID‐19) pandemic, the clinical manifestations of the virus have undergone many changes. Recently, there have been many reports on gastrointestinal symptoms in COVID‐19 patients. This study is aimed to perform a detailed phylogenetic study and assessment of different SNVs in the RNA genome of viruses isolated from fecal samples of patients with COVID‐19 who have gastrointestinal symptoms, which can help better understand viral pathogenesis. In the present study, 20 fecal samples were collected by written consent from COVID‐19 patients. According to the manufacturer's protocol, virus nucleic acid was extracted from stool samples and the SARS‐CoV‐2 genome presence in stool samples was confirmed by RT–PCR assay. Three viral genes, S, nsp12, and nsp2, were amplified using the reverse transcription polymerase chain reaction (RT–PCR) method and specific primers. Multiple sequencing alignment (MSA) was performed in the CLC word bench, and a phylogenetic tree was generated by MEGA X based on the neighbor‐joining method. Of all cases, 11 (55%) were males. The mean age of the patients was 33.6 years. Diabetes (70%) and blood pressure (55%) were the most prevalent comorbidities. All 20 patients were positive for SARS‐CoV‐2 infection in respiratory samples. Molecular analysis investigation among 20 stool samples revealed that the SARS‐CoV‐2 genome was found among 10 stool samples; only three samples were used for sequencing. The polymorphism and phylogenetic analysis in SARS‐CoV‐2 showed great similarity among all of the evaluated genes with the Wuhan reference sequence and all of the current variants of concern (VOCs). The current study represents a great similarity in polymorphism and phylogenetic analysis of the SARS‐CoV‐2 isolates with the Wuhan reference sequence and all of the current VOC in the particular evaluated partial sequences of S, nsp12, and nsp2.

Escherichia coli Clonal Variability Based on Genetic Diversity Pattern with Enterobacterial Repetitive Intergenic Consensus-Polymerase Chain Reaction Methods for Traveler’s Diarrhea Cases in Bali

BACKGROUND: Bali is a favorite tourism destination in the world. As a major tourist destination, the incidence of illness that afflicts tourists greatly affects the image of tourism. Diarrhea is a health problem that is most often experienced and is a major obstacle for foreign tourists when traveling, especially to Bali. Escherichia coli (E. coli) bacteria cause diarrhea more often than viruses in some developing countries. Genetic differences can affect the characteristics of E. coli, especially in relation to the medical field. AIM: We would like to assess the genetic diversity of the different pathogenic E. coli from various clinical isolates including those from traveler’s diarrhea in Bali, Indonesia. MATERIALS AND METHODS: One of the molecular techniques used in this study is to use enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR). The sample in this study was the feces of foreign tourists with traveler’s diarrhea in Bali. This study carried out research procedures in the form of Isolation of E. coli genome DNA from culture, amplification of E. coli 16S rRNA encoding genes, sequencing of E. coli 16S rRNA encoding genes, phylogenetic tree construction, and then analysis of E. coli genetic diversity with ERIC-PCR sequences. RESULTS: The results showed that the ERIC-PCR method was more discriminatory than other methods to analyze the genetic diversity of E. coli from fecal samples of patients with traveler’s diarrhea. It was found that clonal variability based on the genetic similarity of all sample E. coli isolates varied from 0% to 100%. CONCLUSIONS: This shows that the source of transmission and the strains of E. coli that cause it comes from diverse populations.

Analysis of Faecal Microbiota and Small ncRNAs in Autism: Detection of miRNAs and piRNAs with Possible Implications in Host-Gut Microbiota Cross-Talk.

Intestinal microorganisms impact health by maintaining gut homeostasis and shaping the host immunity, while gut dysbiosis associates with many conditions, including autism, a complex neurodevelopmental disorder with multifactorial aetiology. In autism, gut dysbiosis correlates with symptom severity and is characterised by a reduced bacterial variability and a diminished beneficial commensal relationship. Microbiota can influence the expression of host microRNAs that, in turn, regulate the growth of intestinal bacteria by means of bidirectional host-gut microbiota cross-talk. We investigated possible interactions among intestinal microbes and between them and host transcriptional modulators in autism. To this purpose, we analysed, by “omics” technologies, faecal microbiome, mycobiome, and small non-coding-RNAs (particularly miRNAs and piRNAs) of children with autism and neurotypical development. Patients displayed gut dysbiosis related to a reduction of healthy gut micro- and mycobiota as well as up-regulated transcriptional modulators. The targets of dysregulated non-coding-RNAs are involved in intestinal permeability, inflammation, and autism. Furthermore, microbial families, underrepresented in patients, participate in the production of human essential metabolites negatively influencing the health condition. Here, we propose a novel approach to analyse faeces as a whole, and for the first time, we detected miRNAs and piRNAs in faecal samples of patients with autism.

Prolonged Shedding of SARS-CoV-2 in Feces of COVID-19 Positive Patients: Trends in Genomic Variation in First and Second Wave.

The main route of the transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are through respiratory pathways and close contact of human-to-human. While information about other modes of transmission is comparatively less, some published literature supporting the likelihood of a fecal-oral mode of transmission has been accumulating. The diagnosis of SARS-COV-2 infected cases is based on the real-time reverse transcription-PCR (RT-PCR). The fecal excretion of SARS-COV-2 has been reported frequently, however, the role of fecal viral load with the severity of disease is not yet clear. Our study focused on the investigation of SARS-CoV-2 shedding in the fecal samples of patients with coronavirus disease 2019 (COVID-19). A total of 280 RT-PCR-positive patients were enrolled, among them 15.4% had gastrointestinal (GI) symptoms. It was shown that 62% of the patients were positive for SARS-CoV-2 RNA in fecal specimens. This positivity was not related to the presence of GI symptoms and the severity of disease. The next generation sequencing [NGS] of SARS-CoV-2 from fecal samples of patients was performed to analyze mutational variations. Findings from this study not only emphasized the potential presence of SARS-CoV-2 in feces, but also its continuing mutational changes and its possible role in fecal-oral transmission.

Preoperative Status of Gut Microbiota Predicts Postoperative Delirium in Patients With Gastric Cancer.

IntroductionPost-operative delirium (POD) is a serious complication which occurs after surgery, especially in the elderly undergoing abdominal surgery. Increasing evidence has revealed an association between the gut microbiota and psychological disorders involving the “brain-gut” axis. However, the association between the pathogenesis of POD after abdominal surgery in aging and composition of the gut microbiota remains unclear.MethodsForty patients (≥65 years old) who underwent abdominal surgery were included in the study. Twenty patients had POD, whereas 20 patients did not. POD was diagnosed and assessed using the confusion assessment method (CAM) during the postoperative period. Total DNA fractions were extracted from all fecal samples of patients. 16S rRNA sequencing was performed to determine the composition of the gut microbiota. The quality of the samples was determined by calculating the α- and β-diversities.ResultsThe α- and β-diversities indicated that the samples were eligible for detection and comparison. We observed multiple differentially abundant bacteria in patients with and without POD. Generally, Proteobacteria, Enterbacteriaceae, Escherichia shigella, Klebsiella, Ruminococcus, Roseburia, Blautia, Holdemanella, Anaerostipes, Burkholderiaceae, Peptococcus, Lactobacillus, and Dorea were abundant in the POD cohort, whereas Streptococcus equinus and Blautia hominis were abundant in the control cohort. The results of receiver operating characteristic (ROC) curve analysis showed that the area under the curve (AUC) of Escherichia shigella was 0.75. Phenotype prediction showed that the gut microbiota may influence POD by altering the tolerance to oxidative stress.ConclusionThere were significant associations between the pathogenesis of POD and composition of the gut microbiota. Escherichia shigella are promising diagnostic bacterial species for predicting POD onset after abdominal surgery in elderly people.Clinical Trial Registrationhttp://www.chictr.org.cn/index.aspx, Chinese Clinical Trial Registry ChiCTR200030131.

Comparison of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolates From Rooks (Corvus frugilegus) and Contemporary Human-Derived Strains: A One Health Perspective.

During winter, a large number of rooks gather and defecate at the park of a university clinic. We investigated the prevalence of extended-spectrum beta-lactamase (ESBL)–producing Escherichia coli in these birds and compared recovered isolates with contemporary human isolates. In 2016, fecal samples were collected from 112 trap-captured rooks and investigated for presence of ESBL producers using eosin methylene blue agar supplemented by 2 mg/L cefotaxime; 2,455 contemporary human fecal samples of patients of the clinics sent for routine culturing were tested similarly. In addition, 42 ESBL-producing E. coli isolates collected during the same period from inpatients were also studied. ESBL genes were sought for by PCR and were characterized by sequencing; E. coli ST131 clones were identified. Epidemiological relatedness was determined by pulsed-field gel electrophoresis and confirmed using whole genome sequencing in selected cases. Thirty-seven (33%) of sampled rooks and 42 (1.7%) of human stools yielded ESBL-producing E coli. Dominant genes were blaCTX–M–55 and blaCTX–M–27 in corvid, blaCTX–M–15 and blaCTX–M–27 in human isolates. ST162 was common among rooks. Two rook-derived E. coli belonged to ST131 C1-M27, which was also predominant (10/42) among human fecal and (15/42) human clinical isolates. Another potential link between rooks and humans was a single ST744 rook isolate grouped with one human fecal and three clinical isolates. Despite possible contact, genotypes shared between rooks and humans were rare. Thus, rooks are important as long-distance vectors and reservoirs of ESBL-producing E. coli rather than direct sources of infections to humans in our setting.

Molecular diagnosis of intestinal microsporidia infection in HIV/AIDS-patients in Zahedan city, Southeast of Iran.

Microsporidia belong to the intracellular spore-like pathogen, that can cause infection in invertebrates and vertebrates, including humans. Encephalitozoon spp. and Enterocytozoon bieneusi, are important causes of chronic diarrhea, especially in patients with HIV/AIDS. Therefore, in this study, modified trichrome staining (MTS) and nested polymerase chain reaction (nested PCR) methods were used for the diagnosis of common intestinal microsporidia in faecal samples of patients with HIV/AIDS in Zahedan, southeastern Iran, for the first time. Stool samples were collected from 50 HIV/AIDS-infected patients with gastrointestinal symptoms whose infections were confirmed by serology test. Prepared smears from each stool sample were stained using the MTS method. Nested PCR was used to amplify 440 bp and 629 bp fragments of 16S rRNA genes in E. bieneusi and Encephalitozoon spp., respectively. Based on the MTS method and the nested PCR, 8 (16%) and 12 (24%) stool samples were positive, respectively. According to the results of nested PCR, eight, three, and one case were infected with E. bieneusi, Encephalitozoon spp., and both of them, respectively. Findings indicated microsporidiosis in HIV/AIDS-infected patients in Zahedan is an important health problem. Therefore, this opportunistic microorganism in HIV/AIDS-infected patients should be diagnosed using sensitive and accurate methods.

Early melanoma invasivity correlates with gut fungal and bacterial profiles.

SummaryBackgroundThe microbiome is emerging as a crucial player of the immune checkpoint in cancer. Melanoma is a highly immunogenic tumour, and the composition of the gut microbiome has been correlated to prognosis and evolution of advanced melanoma and proposed as a biomarker for immune checkpoint therapy.ObjectivesWe investigated the gut fungal and bacterial compositions in early‐stage melanoma and correlated microbial profiles with histopathological features.MethodsSequencing of bacterial 16S rRNA and the fungal internal transcribed spacer region was performed on faecal samples of patients with stage I and II melanoma, and healthy controls. A meta‐analysis with gut microbiota data from patients with metastatic melanoma was also carried out.ResultsWe found a combination of gut fungal and bacterial profiles significantly discriminating patients with melanoma from controls. In patients with melanoma, we observed an abundance of Prevotella copri and yeasts belonging to the order Saccharomycetales. We found that the bacterial and fungal community correlated to melanoma invasiveness, whereas the specific fungal profile correlated to melanoma regression. Bacteroides was identified as general marker of immunogenicity, being shared by regressive and invasive melanoma. In addition, the bacterial communities in patients with stage I and II melanoma were different in structure and richer than those from patients with metastatic melanoma.ConclusionsThe composition of the gut microbiota in early‐stage melanoma changes along the gradient from in situ to invasive (and metastatic) melanoma. Changes in the microbiota and mycobiota are correlated to the histological features of early‐stage melanoma, and to the clinical course and response to immune therapies of advanced‐stage melanoma, through direct or indirect immunomodulation.