Bahtiyar Yilmaz

Gut Microbiota Elicits a Protective Immune Response against Malaria Transmission

Summary Glycosylation processes are under high natural selection pressure, presumably because these can modulate resistance to infection. Here, we asked whether inactivation of the UDP-galactose:β-galactoside-α1-3-galactosyltransferase (α1,3GT) gene, which ablated the expression of the Galα1-3Galβ1-4GlcNAc-R (α-gal) glycan and allowed for the production of anti-α-gal antibodies (Abs) in humans, confers protection against Plasmodium spp. infection, the causative agent of malaria and a major driving force in human evolution. We demonstrate that both Plasmodium spp. and the human gut pathobiont E. coli O86:B7 express α-gal and that anti-α-gal Abs are associated with protection against malaria transmission in humans as well as in α1,3GT-deficient mice, which produce protective anti-α-gal Abs when colonized by E. coli O86:B7. Anti-α-gal Abs target Plasmodium sporozoites for complement-mediated cytotoxicity in the skin, immediately after inoculation by Anopheles mosquitoes. Vaccination against α-gal confers sterile protection against malaria in mice, suggesting that a similar approach may reduce malaria transmission in humans. PaperFlick

Nlrp6- and ASC-Dependent Inflammasomes Do Not Shape the Commensal Gut Microbiota Composition

&NA; The gut microbiota regulate susceptibility to multiple human diseases. The Nlrp6‐ASC inflammasome is widely regarded as a hallmark host innate immune axis that shapes the gut microbiota composition. This notion stems from studies reporting dysbiosis in mice lacking these inflammasome components when compared with non‐littermate wild‐type animals. Here, we describe microbial analyses in inflammasome‐deficient mice while minimizing non‐genetic confounders using littermate‐controlled Nlrp6‐deficient mice and ex‐germ‐free littermate‐controlled ASC‐deficient mice that were all allowed to shape their gut microbiota naturally after birth. Careful microbial phylogenetic analyses of these cohorts failed to reveal regulation of the gut microbiota composition by the Nlrp6‐ and ASC‐dependent inflammasomes. Our results obtained in two geographically separated animal facilities dismiss a generalizable impact of Nlrp6‐ and ASC‐dependent inflammasomes on the composition of the commensal gut microbiota and highlight the necessity for littermate‐controlled experimental design in assessing the influence of host immunity on gut microbial ecology. HighlightsNon‐littermate controls fail to define host genetic impacts on the gut microbiotaLittermate separation does not reveal ASC‐Nlrp6 impacts on the gut microbiotaLifetime littermate separation does not reveal Nlrp6 impacts on DSS colitis &NA; Inflammasomes were proposed to shape gut ecology based on dysbiosis in mutant mice versus non‐littermate wild‐types. Mamantopoulos et al. show that inflammasomes do not affect gut microbiota composition when controlling for non‐genetic confounders. This finding dismisses the suggested role for inflammasomes in controlling host health through regulation of intestinal ecology.

Microbiota Control of Malaria Transmission

Stable mutualistic interactions between multicellular organisms and microbes are an evolutionarily conserved process with a major impact on host physiology and fitness. Humans establish such interactions with a consortium of microorganisms known as the microbiota. Despite the mutualistic nature of these interactions, some bacterial components of the human microbiota express immunogenic glycans that elicit glycan-specific antibody (Ab) responses. The ensuing circulating Abs are protective against infections by pathogens that express those glycans, as demonstrated for Plasmodium, the causative agent of malaria. Presumably, a similar protective Ab response acts against other vector-borne diseases.

IgA Function in Relation to the Intestinal Microbiota

IgA is the dominant immunoglobulin isotype produced in mammals, largely secreted across the intestinal mucosal surface. Although induction of IgA has been a hallmark feature of microbiota colonization following colonization in germ-free animals, until recently appreciation of the function of IgA in host-microbial mutualism has depended mainly on indirect evidence of alterations in microbiota composition or penetration of microbes in the absence of somatic mutations in IgA (or compensatory IgM). Highly parallel sequencing techniques that enable high-resolution analysis of either microbial consortia or IgA sequence diversity are now giving us new perspectives on selective targeting of microbial taxa and the trajectory of IgA diversification according to induction mechanisms, between different individuals and over time. The prospects are to link the range of diversified IgA clonotypes to specific antigenic functions in modulating the microbiota composition, position and metabolism to ensure host mutualism.

D-lactic Acidosis: Successful Suppression of D-lactate–Producing Lactobacillus by Probiotics

Close monitoring of the stool microbial composition via 16S ribosomal RNA sequencing in a pediatric patient with SBS and D-lactic acidosis reveals treatment-specific changes. Intestinal microbiota composition in children with short bowel syndrome (SBS) is an important factor influencing the clinical outcome. An increase of D-lactate–producing bacteria can lead to D-lactic acidosis, also referred to as D-lactate encephalopathy, with severe neurologic impairment. Antibiotic treatments for D-lactic acidosis in children with SBS offer often only short-term relief. Here, we present the case of a boy with SBS who developed recurrent episodes of D-lactic acidosis even under continuous cycling antibiotic treatment. Microbiological analyses were used to detect the presence of D-lactate–producing Lactobacillus species in the stool samples. A probiotic cocktail was introduced to alter the intestinal microbiota. During follow-up under treatment with probiotics, the patient remained stable, and there was no additional need for antibiotic therapy for more than a year. Stool composition of the patient was sequenced regularly over that period. His microbiota profile changed completely in species richness, and a clustering of species according to probiotic usage was seen. Importantly, D-lactate–producing Lactobacillus strains disappeared within a few weeks after probiotic introduction and were no longer detected in the subsequent follow-up specimens.

Antibodies Set Boundaries Limiting Microbial Metabolite Penetration and the Resultant Mammalian Host Response

SUMMARY Although the mammalian microbiota is well contained within the intestine, it profoundly shapes development and metabolism of almost every host organ. We questioned the range and depth of microbial metabolite penetration into the host, and how this is modulated by intestinal immunity. Chemically identical microbial and host metabolites were distinguished by stable isotope tracing from 13C‐labeled live non‐replicating Escherichia coli, differentiating 12C host isotopes with high‐resolution mass spectrometry. Hundreds of endogenous microbial compounds penetrated 23 host tissues and fluids after intestinal exposure: subsequent 12C host metabolome signatures included lipidemia, reduced glycolysis, and inflammation. Penetrant bacterial metabolites from the small intestine were rapidly cleared into the urine, whereas induced antibodies curtailed microbial metabolite exposure by accelerating intestinal bacterial transit into the colon where metabolite transport mechanisms are limiting. Pervasive penetration of microbial molecules can cause extensive host tissue responses: these are limited by immune and non‐immune intestinal mucosal adaptations to the microbiota. Graphical Abstract Figure. No caption available. HIGHLIGHTSMetabolites from mutualistic bacteria broadly penetrate host tissues and organsBacterial metabolites induce widespread host metabolic and immunological responsesThe small intestine is highly susceptible to host‐microbial metabolomic exchangeSecretory immunoglobulins accelerate microbial clearance from the small intestine &NA; Bacteria‐derived metabolites pervade the mammalian host, shaping immunity and metabolism. Using stable isotope tracing, Uchimura and colleagues profile the scope and depth of host tissue penetration by bacterial metabolites. Extensive host immune and metabolic responses to microbial metabolite penetration are constrained by secretory antibodies that limit microbial small‐intestinal dwell time.

The presence of genetic risk variants within PTPN2 and PTPN22 is associated with intestinal microbiota alterations in Swiss IBD cohort patients

Background Genetic risk factors, intestinal microbiota and a dysregulated immune system contribute to the pathogenesis of inflammatory bowel disease (IBD). We have previously demonstrated that dysfunction of protein tyrosine phosphatase non-receptor type 2 (PTPN2) and PTPN22 contributes to alterations of intestinal microbiota and the onset of chronic intestinal inflammation in vivo. Here, we investigated the influence of PTPN2 and PTPN22 gene variants on intestinal microbiota composition in IBD patients. Methods Bacterial DNA from mucosa-associated samples of 75 CD and 57 UC patients were sequenced using 16S rRNA sequencing approach. Microbial analysis, including alpha diversity, beta diversity and taxonomical analysis by comparing to PTPN2 (rs1893217) and PTPN22 (rs2476601) genotypes was performed in QIIME, the phyloseq R package and MaAsLin pipeline. Results In PTPN2 variant UC patients, we detected an increase in relative abundance of unassigned genera from Clostridiales and Lachnospiraceae families and reduction of Roseburia when compared to PTPN2 wild-type (WT) patients. Ruminoccocus was increased in PTPN22 variant UC patients. In CD patients with severe disease course, Faecalibacterium, Bilophila, Coprococcus, unclassified Erysipelotrichaeceae, unassigned genera from Clostridiales and Ruminococcaceae families were reduced and Bacteroides were increased in PTPN2 WT carriers, while Faecalibacterium, Bilophila, Coprococcus, and Erysipelotrichaeceae were reduced in PTPN22 WT patients when compared to patients with mild disease. In UC patients with severe disease, relative abundance of Lachnobacterium was reduced in PTPN2 and PTPN22 WT patients, Dorea was increased in samples from PTPN22 WT carriers and an unassigned genus from Ruminococcaceae gen. was increased in patients with PTPN2 variant genotype. Conclusions We identified that IBD-associated genetic risk variants, disease severity and the interaction of these factors are related to significant alterations in intestinal microbiota composition of IBD patients.

Antibodies that lIgAte our intestinal microbes

Perturbations in gut microbiota of IgA-deficient humans provide insight into how secretory IgA shapes microbiota composition (see the related research article by Fadlallah et al.). Perturbations in gut microbiota of IgA-deficient humans provide insight into how secretory IgA shapes microbiota composition.

A new cost and time effective method for multilocus microsatellite typing (MLMT) studies: Application of Leishmania tropica isolates and clinical samples from Turkey

Molecular techniques are widely used in the field of parasitology to identify the genetic profile of the microbiological agents. Microsatellite typing studies are comprised of the amplification of polymorphic markers to analyze the fragment sizes using bioinformatics tools. Current methods need fluorescently labeled primers and size markers to obtain fragment peaks in ABI PRISM® systems and due to low discrimination power of gel-electrophoresis, it is not possible to differentiate primer-dimers from small fragments In the present study, we designed a new method for fragment analysis studies, which reduce the time by eliminating the classical PCR, the gel-electrophoresis and the preparation steps of fragment analysis. Ten previously studied Leishmania tropica strains and one Giemsa-stained slide were tested by new method and obtained fragment peaks were compared to the previous data obtained from ABI PRISM® system. Overall twelve makers were tested and the signal peak from each fragment was compared to classical ABI PRISM®-based fragment analysis and noted as identical. The new protocol is time saving, cost effective, and eliminates the human error comparing to classical MLMT analysis protocol. We believe that this method enables the easy detection of the fragment lengths without having bioinformatics experience and the obtained data can be easily shared with other laboratories.