Gut Pathogens

Sphingolipids are important for innate immune response to eliminate infected pathogens and involved in autophagy. On the other hand, nucleotide-binding oligomerization domain-containing protein 2 (NOD2) served as an intracellular pattern recognition receptor to enhance host defense by inducing autophagy and the production of antimicrobial peptides, such as human beta-defensin-2 (hBD-2). However, the role of sphingolipids in Salmonella-induced autophagy and hBD-2 response in intestinal epithelial cells has not been previously elucidated. Salmonella typhimurium wild-type strain SL1344 was used to infect SW480, an intestinal epithelial cell. hBD-2 and interleukin-8 (IL-8) mRNA expressions were assessed in SW480 cells using RT-PCR, and intracellular signaling pathways and autophagy protein expression were analyzed by Western blot in SW480 cells in the presence or absence of inhibitors or transfected with siRNA. We demonstrated that inhibition of de novo sphingolipid synthesis repressed the membrane recruitment of NOD2 and autophagy-related protein 16-like 1 (Atg16L1), suppressed Salmonella-induced autophagic protein LC3-II expression, and reduced NOD2-mediated hBD-2 response in Salmonella-infected SW480 cells. Contrasting to the utilization of membrane cholesterol on maintenance of Salmonella-containing vacuoles and anti-inflammation by Salmonella, sphingolipids act on epithelial defense against the invasive pathogen. Our results offer mechanistic insights on the role of de novo sphingolipid synthesis in the innate immunity of intestinal epithelial cells to Salmonella infection. The pharmaceuticals enhancing or diet enriched with sphingolipids may induce the dual anti-bacterial mechanisms. The role of de novo sphingolipid synthesis on inflammatory bowel disease is deserved to be further investigated.

Mouse infection studies have shown that interferon-γ (IFN-γ), a T helper 1 (Th1) cytokine, is required for the development of severe pathology induced by chronic Helicobacter infection. This finding is largely based on studies performed using mice that have polarised Th1 responses i.e. C57BL/6 animals. The current work aims to investigate the role of IFN-γ in Helicobacter-induced inflammation in BALB/c mice which have Th2-polarised immune responses. At 7 months post-infection with Helicobacter felis, IFN-γ deficiency in BALB/c mice had no significant effect on H. felis colonisation levels in the gastric mucosa, nor on humoral responses, or gastritis severity. Ifng −/− animals with chronic H. felis infection did, however, develop significantly fewer lymphoid follicle lesions, as well as increased IL-4 splenocyte responses, when compared with infected Ifng +/+ mice (P = 0.015 and P = 0.0004, respectively). The work shows that in mice on a BALB/c background, IFN-γ is not required for bacterial clearance, antibody responses, nor gastric inflammation. Conversely, IFN-γ appears to play a role in the development of gastric lymphoid follicles, which are precursor lesions to mucosa-associated lymphoid tissue (MALT) lymphoma. This study highlights the importance of mouse host background on the susceptibility to Helicobacter-induced pathologies.

In the original version of this article [1], published on 17 November 2017, Table 2 contains an error: the first “T” in the first sequence in the column ‘Consensus direct repeats (CDRs) sequences’ has been incorrectly underlined. In Table 2, the underlining indicates the Consensus sequence

Virus rotavirus (RV) là một trong những nguyên nhân hàng đầu gây tiêu chảy và tỷ lệ tử vong ở trẻ em trên toàn thế giới. Virus này gây ra viêm dạ dày ruột cấp tính với các triệu chứng nôn vừa đến nặng, tiêu chảy, mất nước và sốt. Sự rối loạn vi sinh vật do nhiễm RV có thể ảnh hưởng đáng kể đến tiên lượng bệnh và sự phát triển của các bệnh mạn tính khác. Hệ vi sinh vật đường ruột đóng vai trò quan trọng trong phản ứng miễn dịch đường tiêu hóa đối với vắc xin rotavirus (RVV) và cần có thêm nghiên cứu để làm rõ. Nghiên cứu hiện tại đánh giá hệ vi sinh vật đường ruột của trẻ em dương tính với RV và so sánh biểu hiện viêm dạ dày ruột ở trẻ em nhập viện tại Trung tâm Cấp cứu Nhi khoa, Tập đoàn Y tế Hamad, Doha, Qatar. Mẫu phân đã được thu thập từ ba mươi chín trẻ em dương tính với RV và tám trẻ em khỏe mạnh trong nhóm kiểm soát. Phân tích chuỗi 16S rRNA được tiến hành bằng nền tảng Illumina MiSeq. Dữ liệu cho thấy sự gia tăng đáng kể về sự đa dạng của hệ vi sinh vật với sự phong phú tương đối cao của ngành Proteobacteria (p = 0.031), Fusobacteria (p = 0.044) và giống Streptococcus (p ≤ 0.001) trong nhóm nhiễm so với nhóm kiểm soát. Tương tự, một mô hình phân cụm vùng (PERMANOVA p = 0.01) và độ phong phú loài cao hơn (entropy Shannon p = 0.018) đã được quan sát ở các trẻ em đã nhận hai liều vắc xin RVV so với nhóm không tiêm hoặc nhóm một liều. Những thay đổi trong hệ vi sinh vật này thể hiện sự phong phú quá mức của ngành Bacteroidetes (p = 0.003) và Verrucomicrobia (p ≤ 0.001), và sự biểu hiện thấp hơn của họ Enterobacteriaceae trong nhóm hai liều RVV. Tuy nhiên, thành phần hệ vi sinh vật không liên quan đến tiêu chảy, nôn mửa và các thông số khác của viêm dạ dày ruột. Những quan sát này khẳng định các dấu hiệu vi sinh vật quan trọng của RVV, phụ thuộc liều, và gợi ý việc điều chỉnh những vi sinh vật này như một phương pháp mới để cải thiện hiệu quả của RVV. Cần tiến hành các nghiên cứu tiếp theo để điều tra trạng thái miễn dịch của những bệnh nhân này cũng như điều tra cơ chế nhằm nâng cao tỷ lệ seroconversion của RVV.

Adherent invasive Escherichia coli (AIEC) are suspected to be involved in the pathogenesis of inflammatory bowel diseases. Since AIEC was first described in 1999, despite important progress on its genomic and immune characterizations, some crucial questions remain unanswered, such as whether there exists a natural reservoir, or whether there is asymptomatic carriage. The ECOR collection, including E. coli strains isolated mainly from the gut of healthy humans and animals, constitutes an ideal tool to investigate AIEC prevalence in healthy condition. A total of 61 E. coli strains were examined for characteristics of AIEC. The adhesion, invasion and intramacrophage replication capabilities (AIEC phenotype) of 61 intestinal E. coli strains were determined. The absence of virulence-associated diarrheagenic E. coli pathotypes (EPEC, ETEC, EIEC, EHEC, DAEC, EAEC), and uropathogenic E. coli was checked. Out of 61 intestinal strains, 13 (21%) exhibit the AIEC phenotype, 7 are from human origin and 6 are from animal origin. Prevalence of AIEC strains is about 24 and 19% in healthy humans and animals respectively. These strains are highly genetically diverse as they are distributed among the main described phylogroups. Among E. coli strains from the ECOR collection, we also detected strains able to detach I-407 cells. Our study described for the first time AIEC strains isolated from the feces of healthy humans and animals.

Gut microbiota is closely associated with host health and disease occurrence. Host genetic factor plays an important role in shaping gut microbial communities. The specific mechanism of host-regulated gene expression affecting gut microbiota has not been elucidated yet. Here we conducted a transcriptome-wide association study (TWAS) for gut microbiota by leveraging expression imputation from large-scale GWAS data sets. TWAS detected multiple tissue-specific candidate genes for gut microbiota, such as FUT2 for genus Bifidobacterium in transverse colon (PPERM.ANL = 1.68 × 10–3) and SFTPD for an unclassified genus of Proteobacteria in transverse colon (PPERM.ANL = 5.69 × 10–3). Fine mapping replicated 3 candidate genes in TWAS, such as HELLS for Streptococcus (PIP = 0.685) in sigmoid colon, ANO7 for Erysipelotrichaceae (PIP = 0.449) in sigmoid colon. Functional analyses detected 94 significant GO terms and 11 pathways for various taxa in total, such as GO_NUCLEOSIDE_DIPHOSPHATASE_ACTIVITY for Butyrivibrio (FDR P = 1.30 × 10–4), KEGG_RENIN_ANGIOTENSIN_SYSTEM for Anaerostipes (FDR P = 3.16 × 10–2). Literature search results showed 12 genes prioritized by TWAS were associated with 12 diseases. For instance, SFTPD for an unclassified genus of Proteobacteria was related to atherosclerosis, and FUT2 for Bifidobacterium was associated with Crohn’s disease. Our study results provided novel insights for understanding the genetic mechanism of gut microbiota, and attempted to provide clues for revealing the influence of genetic factors on gut microbiota for the occurrence and development of diseases.

The emergence of the novel coronavirus SARS-CoV-2, which causes severe respiratory tract infections in humans (COVID-19), has become a global health concern. One of the most worrying features of COVID-19 is a phenomenon known as the “cytokine storm”, which is a rapid overreaction of the immune system. Additionally, coagulation abnormalities, thrombocytopenia and digestive symptoms, including anorexia, vomiting, and diarrhea, are often observed in critically ill patients with COVID-19. Baker’s yeast β-glucan, a natural immunomodulatory component derived from Saccharomyces cerevisiae, primes the immune system to respond better to any microbial infection. Our previous studies have shown that oral administration of yeast β-glucans decreased the diarrhoea, modulated cytokine expression, and reduced the intestinal inflammation. Additionally, we showed that β-glucan fractions decreased coagulation in plasma and reduced the activation of platelets. During the period of home confinement facing individuals during the COVID-19 pandemic, our immune defence could be weakened by different factors, including stress, anxiety and poor nutrition, while a healthy diet rich in vitamins C and D can reinforce the immune defence and reduce the risk of microbial infections. Additionally, β-glucan can be used to strengthen the immune defence in healthy individuals prior to any possible viral infections. This short review focuses on the role of baker’s yeast β-glucan, with a healthy diet rich in natural vitamins C and D, in addition to a healthy gut microbiota can provide synergistic immune system support, helping the body to naturally defend prior to respiratory virus infections, until stronger options such as vaccines are available.

Gut microbiota manipulation may be a potential therapeutic target to reduce host energy storage. There is limited information about the effects of probiotics/synbiotics on intestinal microbiota composition in children and adolescents with obesity. The objective of this randomized double-blind placebo-controlled trial was to test the effects of a multispecies synbiotic on intestinal microbiota composition in children and adolescents with exogenous obesity. Children with exogenous obesity were managed with a standard diet and increased physical activity and were randomly allocated into two groups at a ratio of 1:1; the 1st group received synbiotic supplementation (probiotic mixture including Lactobacillus acidophilus, Lacticaseibacillus. rhamnosus, Bifidobacterium bifidum, Bifidobacterium longum, Enterococcus faecium (total 2.5 × 109 CFU/sachet) and fructo-oligosaccharides (FOS; 625 mg/sachet) for 12 weeks; the 2nd group received placebo once daily for 12 weeks. Fecal samples were obtained before and at the end of the 12-week intervention to characterize the changes in the gut microbiota composition. Detailed metagenomic and bioinformatics analyses were performed. Before the intervention, there were no significant differences in alpha diversity indicators between the synbiotic and placebo groups. After 12 weeks of intervention, the observed taxonomic units and Chao 1 were lower in the synbiotic group than at baseline (p < 0.001 for both). No difference for alpha diversity indicators was observed in the placebo group between baseline and 12 weeks of intervention. At the phylum level, the intestinal microbiota composition of the study groups was similar at baseline. The major phyla in the synbiotic group were Firmicutes (66.7%) and Bacteroidetes (18.8%). In the synbiotic group, the Bacteroidetes phylum was higher after 12 weeks than at baseline (24.0% vs. 18.8%, p < 0.01). In the synbiotic group, the Firmicutes/Bacteroidetes ratio was 3.54 at baseline and 2.75 at 12 weeks of intervention (p < 0.05). In the placebo group, the Firmicutes/Bacteroidetes ratio was 4.70 at baseline and 3.54 at 12 weeks of intervention (p < 0.05). After 12 weeks of intervention, the Firmicutes/Bacteroidetes ratio was also lower in the synbiotic group than in the placebo group (p < 0.05). In the synbiotic group, compared with the baseline, we observed a statistically significant increase in the genera Prevotella (5.28–14.4%, p < 0.001) and Dialister (9.68–13.4%; p < 0.05). Compared to baseline, we observed a statistically significant increase in the genera Prevotella (6.4–12.4%, p < 0.01) and Oscillospira (4.95% vs. 5.70%, p < 0.001) in the placebo group. In the synbiotic group, at the end of the intervention, an increase in Prevotella, Coprococcus, Lachnospiraceae (at the genus level) and Prevotella copri, Coprococcus eutactus, Ruminococcus spp. at the species level compared to baseline (predominance of Eubacterium dolichum, Lactobacillus ruminis, Clostridium ramosum, Bulleidia moorei) was observed. At the end of the 12th week of the study, when the synbiotic and placebo groups were compared, Bacteroides eggerthi species were dominant in the placebo group, while Collinsella stercoris species were dominant in the synbiotic group. This study is the first pediatric obesity study to show that a synbiotic treatment is associated with both changes intestinal microbiota composition and decreases in BMI. Trial identifier: NCT05162209 (www.clinicaltrials.gov). What is Known - Gut microbiota manipulation may be a potential therapeutic target to reduce host energy storage. - There are studies on the use of probiotics and prebiotics as a support for treatment in obesity and effects on microbiota composition, but most of these studies were conducted in adult age groups. - Most of the studies on the effects of probiotics and synbiotics on obesity are related to anthropometric measurements, lipid parameters and non-alcoholic fatty liver disease, and there are few studies regarding their effects on intestinal microbiota composition, especially in children. What is New - This study is the first pediatric obesity study to show that a synbiotic use associated with changes intestinal microbiota composition. - In the synbiotic group, at the end of the intervention, an increase in Prevotella, Coprococcus, Lachnospiraceae at the genus level and Prevotella copri, Coprococcus eutactus, Ruminococcus spp. at the species level compared to baseline (predominance of Eubacterium dolichum, Lactobacillus ruminis, Clostridium ramosum, Bulleidia moorei) was observed.

Rapid detection of a wide range of etiologic agents is essential for appropriate treatment and control of gastrointestinal (GI) infections. A variety of microbial species including bacteria, viruses, parasites, and fungi have been recognized as diarrheagenic enteric pathogens. However, multiplex testing of various targets in a single reaction needs further improvement because of its limitation in species and throughput. This study aims at developing and evaluating a DNA microarray-based qualitative multiplexed polymerase chain reaction (PCR) assay, Vibrant GI pathogen panel (GPP), for simultaneous detection of 27 enteric GI pathogenic targets (16 bacteria, 5 viruses, 4 parasites, and 2 fungi) directly from stool specimens. Limits of detection ranged from 102 to 104 cells/mL for bacteria, 102 to 103 cells/mL for parasites, 102 to 103 RNA copies/mL for viruses, and 102 to 103 cells/mL for fungi. Performance characteristics were determined using 27 Quantitative Genomic DNAs, 212 spiked stool specimens, 1067 clinical and archived stool specimens. Overall sensitivity was 95.9% (95% CI 92.4–98.1) and specificity was 100% (95% CI 99.9–100). Polymicrobial detections contained either two or three organisms was 20.2% (35/173) of positive clinical specimens and 3.3% (35/1055) of all clinical specimens. The Vibrant GPP is a comprehensive, high-throughput, and rapid DNA microarray to provide etiologic diagnosis of GI infections in the laboratory setting.