Empiric probiotics are commonly consumed by healthy individuals as means of life quality improvement and disease prevention. However, evidence of probiotic gut mucosal colonization efficacy remains sparse and controversial. We metagenomically characterized the murine and human mucosal-associated gastrointestinal microbiome and found it to only partially correlate with stool microbiome. A sequential invasive multi-omics measurement at baseline and during consumption of an 11-strain probiotic combination or placebo demonstrated that probiotics remain viable upon gastrointestinal passage. In colonized, but not germ-free mice, probiotics encountered a marked mucosal colonization resistance. In contrast, humans featured person-, region- and strain-specific mucosal colonization patterns, hallmarked by predictive baseline host and microbiome features, but indistinguishable by probiotics presence in stool. Consequently, probiotics induced a transient, individualized impact on mucosal community structure and gut transcriptome. Collectively, empiric probiotics supplementation may be limited in universally and persistently impacting the gut mucosa, meriting development of new personalized probiotic approaches.

Probiotics are widely prescribed for prevention of antibiotics-associated dysbiosis and related adverse effects. However, probiotic impact on post-antibiotic reconstitution of the gut mucosal host-microbiome niche remains elusive. We invasively examined the effects of multi-strain probiotics or autologous fecal microbiome transplantation (aFMT) on post-antibiotic reconstitution of the murine and human mucosal microbiome niche. Contrary to homeostasis, antibiotic perturbation enhanced probiotics colonization in the human mucosa but only mildly improved colonization in mice. Compared to spontaneous post-antibiotic recovery, probiotics induced a markedly delayed and persistently incomplete indigenous stool/mucosal microbiome reconstitution and host transcriptome recovery toward homeostatic configuration, while aFMT induced a rapid and near-complete recovery within days of administration. In vitro, Lactobacillus-secreted soluble factors contributed to probiotics-induced microbiome inhibition. Collectively, potential post-antibiotic probiotic benefits may be offset by a compromised gut mucosal recovery, highlighting a need of developing aFMT or personalized probiotic approaches achieving mucosal protection without compromising microbiome recolonization in the antibiotics-perturbed host.

Macrophage migration inhibitory factor (MIF) is an upstream activator of innate immunity that regulates subsequent adaptive responses. It was previously shown that in macrophages, MIF binds to a complex of CD74 and CD44, resulting in initiation of a signaling pathway. In the current study, we investigated the role of MIF in B cell survival. We show that in B lymphocytes, MIF initiates a signaling cascade that involves Syk and Akt, leading to NF-B activation, proliferation, and survival in a CD74-and CD44-dependent manner. Thus, MIF regulates the adaptive immune response by maintaining the mature B cell population.An established paradigm divides the immunologic response into innate and adaptive components, with critical interactions between the two producing normal immunity or immunopathology. The innate response represents the earliest host response to invasive pathogens by cells such as monocytes/ macrophages, whereas the adaptive response includes the development of antigen-specific responses, antibody production, and immunologic memory. Significant attention is currently focused on the molecules that link innate and adaptive immunity, and that may critically regulate immune responses or the development of inflammatory/autoimmune diseases.CD74 is a non-polymorphic type II integral membrane protein that is expressed on antigen presenting cells including macrophages and B cells. It has a short N-terminal cytoplasmic tail of 28 amino acids, followed by a single 24-amino acid transmembrane region and an ϳ150-amino acid lumenal domain. The CD74 chain was considered initially to function mainly as a major histocompatibility complex class II chaperone, which promotes endoplasmic reticulum exit of major histocompatibility complex class II molecules, directs them to endocytic compartments, prevents peptide binding in the endoplasmic reticulum, and contributes to peptide editing in the major histocompatibility complex class II compartment (1). A small proportion of CD74 is modified by the addition of chondroitin sulfate (CD74-CS), and this form of CD74 is expressed on the surface of antigen presenting cells, including monocytes and B cells. Antibody blocking studies additionally have shown that CD74-CS interacts with CD44, which activates a Src-kinase dependent signaling pathway (2).It was previously shown that macrophage migration inhibitory factor (MIF) 3 binds to the CD74 extracellular domain on macrophages, a process that results in initiation of a signaling pathway (3). MIF accounts for one of the first cytokine activities to have been described (4). MIF promotes monocyte/macrophage activation and is required for the optimal expression of tumor necrosis factor, interleukin-1, and prostaglandin E 2 (5-7). MIF-activated macrophages are more phagocytic and better able to destroy intracellular pathogens, such as Leishmania (8, 9). These activating functions have been verified in MIF knock-out mice (6, 10, 11). The role of MIF in adaptive immunity is less well characterized, but neutralization of MIF using specific anti...

Inflammatory bowel diseases involve the dynamic interplay of host genetics, microbiome and inflammatory response. Here, we report that NLRP12, a negative regulator of innate immunity, is reduced in human ulcerative colitis by comparing monozygotic twins and other patient cohorts. In parallel, Nlrp12-deficiency in mice caused increased colonic basal inflammation, leading to a less-diverse microbiome, loss of protective gut commensal strains (Lachnospiraceae) and increased colitogenic strains (Erysipelotrichaceae). Dysbiosis and colitis susceptibility associated with Nlrp12-deficency were reversed equally by treatment with antibodies targeting inflammatory cytokines or by administration of beneficial commensal Lachnospiraceae isolates. Fecal transplants from specific pathogen free reared mice into germ-free Nlrp12-deficient mice showed that NLRP12 and the microbiome each contribute to immune signaling that culminates in colon inflammation. These findings reveal a feed-forward loop where NLRP12 promotes specific commensals that can reverse gut inflammation, while cytokine blockade during NLRP12-deficiency can reverse dysbiosis.

No abstract

Alterations in the gut microbiome have been implicated in the pathogenesis of several immune‐mediated inflammatory diseases such as psoriatic arthritis. This work aimed to characterize the gut microbial signature of patients with active psoriasis as compared with age‐, body mass index‐ and comorbidity‐matched non‐psoriatic controls and to correlate them with differential expression of metabolic pathways. Fecal samples were processed and 16S rRNA was sequenced. PICRUSt was used to perform an analysis of metabolic pathways. Of the 46 participants, 52% (n = 24) suffered from psoriasis. There was a significant difference in β‐diversity between the two groups. Psoriatic patients had a significant increase in the Firmicutes and Actinobacteria phyla as compared with matched controls. At the genus level, psoriatic patients had a unique bacterial composition. At the species level, the psoriatic patients showed significant increases in the relative proportions of (false discovery rate, <0.05) in Ruminoccocus gnavus, Dorea formicigenerans and Collinsella aerofaciens, while Prevotella copri and Parabacteroides distasonis were significantly decreased as compared with controls. PICRUSt analysis revealed increases in metabolic pathways related to lipopolysaccharide function in the psoriatic cohort. These data demonstrate unique fecal microbial and metabolic signatures in psoriatic patients.

No abstract

The LM and MAM are distinct microbial ecosystems that differ significantly from each other in microbial diversity and composition. These two microbial niches should be investigated independently to better understand the role of the intestinal microbiota in health and disease.