The widespread application of next-generation sequencing technologies has revolutionized microbiome research by enabling high-throughput profiling of the genetic contents of microbial communities. How to analyze the resulting large complex datasets remains a key challenge in current microbiome studies. Over the past decade, powerful computational pipelines and robust protocols have been established to enable efficient raw data processing and annotation. The focus has shifted toward downstream statistical analysis and functional interpretation. Here, we introduce MicrobiomeAnalyst, a user-friendly tool that integrates recent progress in statistics and visualization techniques, coupled with novel knowledge bases, to enable comprehensive analysis of common data outputs produced from microbiome studies. MicrobiomeAnalyst contains four modules - the Marker Data Profiling module offers various options for community profiling, comparative analysis and functional prediction based on 16S rRNA marker gene data; the Shotgun Data Profiling module supports exploratory data analysis, functional profiling and metabolic network visualization of shotgun metagenomics or metatranscriptomics data; the Taxon Set Enrichment Analysis module helps interpret taxonomic signatures via enrichment analysis against >300 taxon sets manually curated from literature and public databases; finally, the Projection with Public Data module allows users to visually explore their data with a public reference data for pattern discovery and biological insights. MicrobiomeAnalyst is freely available at http://www.microbiomeanalyst.ca.

The dogma that adaptive immunity is the only arm of the immune response with memory capacity has been recently challenged by several studies demonstrating evidence for memory-like innate immune training. However, the underlying mechanisms and location for generating such innate memory responses in vivo remain unknown. Here, we show that access of Bacillus Calmette-Guérin (BCG) to the bone marrow (BM) changes the transcriptional landscape of hematopoietic stem cells (HSCs) and multipotent progenitors (MPPs), leading to local cell expansion and enhanced myelopoiesis at the expense of lymphopoiesis. Importantly, BCG-educated HSCs generate epigenetically modified macrophages that provide significantly better protection against virulent M. tuberculosis infection than naïve macrophages. By using parabiotic and chimeric mice, as well as adoptive transfer approaches, we demonstrate that training of the monocyte/macrophage lineage via BCG-induced HSC reprogramming is sustainable in vivo. Our results indicate that targeting the HSC compartment provides a novel approach for vaccine development.

The relationship of T follicular helper (TFH) cells to other T helper (Th) subsets is controversial. We find that after helminth infection, or immunization with helminth antigens, reactive lymphoid organs of 4get IL-4/GFP reporter mice contain populations of IL-4/GFP-expressing CD4+ T cells that display the TFH markers CXCR5, PD-1, and ICOS. These TFH cells express the canonical TFH markers BCL6 and IL-21, but also GATA3, the master regulator of Th2 cell differentiation. Consistent with a relationship between Th2 and TFH cells, IL-4 protein production, reported by expression of huCD2 in IL-4 dual reporter (4get/KN2) mice, was a robust marker of TFH cells in LNs responding to helminth antigens. Moreover, the majority of huCD2/IL-4–producing Th cells were found within B cell follicles, consistent with their definition as TFH cells. TFH cell development after immunization failed to occur in mice lacking B cells or CD154. The relationship of TFH cells to the Th2 lineage was confirmed when TFH cells were found to develop from CXCR5− PD-1− IL-4/GFP+ CD4+ T cells after their transfer into naive mice and antigen challenge in vivo.

Mature myeloid cells (macrophages andCD11b IntroductionMyeloid cells, such as macrophages and dendritic cells (DCs), are a prominent constituent of inflammatory infiltrates in the central nervous system (CNS) during multiple sclerosis (MS) and experimental autoimmune encephalomyelitis (EAE). 1,2 These cells not only serve as antigen-presenting cells for the reactivation of infiltrating myelin-reactive CD4 ϩ T cells but are thought to directly inflict tissue damage through secretion of toxic factors, such as reactive oxygen species, proteases, and tumor necrosis factor-␣ (TNF-␣). 3,4 They might also recruit naive myelin-reactive T cells into the effector pool in the context of epitope spreading. 5 We and others have demonstrated that bone marrow-derived CD11c ϩ major histocompatibility complex (MHC) class II ϩ DCs accumulate in the CNS during EAE and have the capacity to polarize naive T cells along encephalitogenic Th1 and Th17 lineages. 2,6 However, the circulating cell that gives rise to CNS-infiltrating DCs and macrophages has yet to be defined. The specific chemokine pathways and adhesion molecule interactions required for infiltration of the CNS by myeloid cells will depend on whether they cross the blood-brain barrier as immature monocytes or as macrophages and DCs. Therefore, identification of the differentiation status of the migrating cell holds implications regarding candidate therapeutic targets in neuroinflammatory diseases, such as multiple sclerosis (MS).Under steady-state conditions, mature myeloid lineages are maintained within lymphoid and peripheral tissues through controlled release of bone marrow progenitors/precursors into the peripheral circulation. 7 In the setting of infection or injury, myeloid cell mobilization is accelerated to meet the demands imposed by the increased turnover of macrophages and DCs at the site of inflammation. 8,9 The pathways underlying expansion of peripheral myeloid cell pools under stress are thought to serve an adaptive role by reinforcing host protection against infectious agents and by promoting wound healing. 8 Conversely, leukocyte-mobilizing pathways might be subverted to sustain target organ inflammation during relapsing or chronic autoimmune disease. For example, the number of macrophages and DCs in the CNS contracts during remissions and rebounds during exacerbations of EAE, suggesting that myeloid precursors might be released at a heightened rate before, or in concert with, clinical disease activity. 10,11 Recently, it was shown that CCL2 expression by nonhematopoetic (likely glial) cells is important for the accumulation of proinflammatory DCs in the CNS during acute EAE. 12 Furthermore, transgenic animals that simultaneously express CCL2 in the CNS and Fms-like tyrosine kinase 3 ligand in the periphery spontaneously develop meningeal and perivascular inflammation in association with an ascending paralysis. The neuroinflammation in this model appears to be primarily driven by myeloid cells and occurs independent of T and B lymphocytes. 13 The receptor ...

Viral respiratory tract infections are the main causative agents of the onset of infection-induced asthma and asthma exacerbations that remain mechanistically unexplained. Here we found that deficiency in signaling via type I interferon receptor led to deregulated activation of group 2 innate lymphoid cells (ILC2 cells) and infection-associated type 2 immunopathology. Type I interferons directly and negatively regulated mouse and human ILC2 cells in a manner dependent on the transcriptional activator ISGF3 that led to altered cytokine production, cell proliferation and increased cell death. In addition, interferon-γ (IFN-γ) and interleukin 27 (IL-27) altered ILC2 function dependent on the transcription factor STAT1. These results demonstrate that type I and type II interferons, together with IL-27, regulate ILC2 cells to restrict type 2 immunopathology.

Interleukin (IL)-4 is the quintessential T helper type 2 (Th2) cytokine produced by CD4+ T cells in response to helminth infection. IL-4 not only promotes the differentiation of Th2 cells but is also critical for immunoglobulin (Ig) G1 and IgE isotype-switched antibody responses. Despite the IL-4–mediated link between Th2 cells and B lymphocytes, the location of IL-4–producing T cells in the lymph nodes is currently unclear. Using IL-4 dual reporter mice, we examined the Th2 response and IL-4 production in the draining mesenteric lymph nodes during infection with the enteric nematode Heligmosomoides polygyrus. We show that although IL-4–competent Th2 cells are found throughout the B and T cell areas, IL-4–producing Th2 cells are restricted to the B cell follicles and associate with germinal centers. Consistent with their localization, IL-4 producers express high levels of CXCR5, ICOS, PD-1, IL-21, and BCL-6, a phenotype characteristic of T follicular helper (Tfh) cells. Although IL-4 was dispensable for the generation of Th2 and Tfh cells, its deletion resulted in defective B cell expansion and maturation. Our report reveals the compartmentalization of Th2 priming and IL-4 production in the lymph nodes during infection, and identifies Tfh cells as the dominant source of IL-4 in vivo.

Murine invariant natural killer T (iNKT) cells provide cognate and non-cognate help for lipid and protein-specific B cells, respectively. However, the long term B cell outcome following cognate iNKT help is currently unknown. We show that cognate iNKT cell help resulted in a B cell differentiation program characterized by extrafollicular plasmablasts, germinal center formation, affinity maturation and a robust primary IgG antibody response that was uniquely dependent on iNKT-derived interleukin 21 (IL-21). However, cognate iNKT cell help did not generate an enhanced humoral memory response. Thus, iNKT cell cognate help for lipid-specific B cells induces a unique signature which is a hybrid of classic T-dependent (TD) and T-independent type 2 (TI-2) B cell responses.

Dendritic cells (DCs) are potent inducers of T cell immunity, and autologous DC vaccination holds promise for the treatment of cancers and chronic infectious diseases. In practice, however, therapeutic vaccines of this type have had mixed success. In this article, we show that brief exposure to inhibitors of mechanistic target of rapamycin (mTOR) in DCs during the period that they are responding to TLR agonists makes them particularly potent activators of naive CD8+ T cells and able to enhance control of B16 melanoma in a therapeutic autologous vaccination model in the mouse. The improved performance of DCs in which mTOR has been inhibited is correlated with an extended life span after activation and prolonged, increased expression of costimulatory molecules. Therapeutic autologous vaccination with DCs treated with TLR agonists plus the mTOR inhibitor rapamycin results in improved generation of Ag-specific CD8+ T cells in vivo and improved antitumor immunity compared with that observed with DCs treated with TLR agonists alone. These findings define mTOR as a molecular target for augmenting DC survival and activation, and document a novel pharmacologic approach for enhancing the efficacy of therapeutic autologous DC vaccination.