bims-bac4me Biomed News
on Microbiome and trained immunity
Issue of 2023‒07‒02
38 papers selected by
Chun-Chi Chang
University Hospital Zurich

  1. Front Immunol. 2023 ;14 1211404
      Introduction: During infection, bone marrow (BM) hematopoiesis is reprogrammed toward myeloid cell production, a mechanism named emergency myelopoiesis. In addition to replenishing myeloid cells, emergency myelopoiesis has been linked to trained immunity, a process that allows enhanced innate immune responses to secondary challenges. Although hematopoietic alterations during tuberculosis (TB) have been described and Mycobacterium tuberculosis may colonize the BM, studies using the mouse model of infection and the laboratory reference strain M. tuberculosis H37Rv have demonstrated limited emergency myelopoiesis and trained immunity.Methods: To further address this issue, we aerosol- infected C57BL/6 mice with high doses of the hypervirulent M. tuberculosis isolate HN878 and monitored alterations to the BM. This experimental model better resembles the human blood immune signature of TB.
    Results and discussion: We found increased frequencies of lineage-Sca-1+cKit+ (LSK) cells and the granulocyte/macrophage progenitor (GMP) population. At the mature cell level, we observed an increase of monocytes and neutrophils in the blood and lung, likely reflecting the increased BM myeloid output. Monocytes or monocyte-derived macrophages recovered from the BM of M. tuberculosis HN878-infected mice did not show signs of trained immunity, suggesting an uncoupling of emergency myelopoiesis and trained immunity in the BM. Surprisingly, M. tuberculosis HN878-induced emergency myelopoiesis was not fully dependent on IFNγ, as mice lacking this cytokine and infected under the same conditions as wild-type mice still presented BM alterations. These data expand our understanding of the immune response to M. tuberculosis and raise awareness of pathogen strain-imposed differences to host responses.
    Keywords:  bone marrow; interferon-gamma; myelopoiesis; trained immunity; tuberculosis
  2. J Allergy Clin Immunol. 2023 Jun 27. pii: S0091-6749(23)00810-2. [Epub ahead of print]
      With the growing body of evidence, it is now clear that not only adaptive immune cells but also innate immune cells can mount a more rapid and potent non-specific immune response to subsequent exposures. This process is known as trained immunity or innate (learned) immune memory. In this review, we discuss the different immune and non-immune cell types of the central and peripheral immune systems which can develop trained immunity. We highlight the intracellular signaling, metabolic and epigenetic mechanisms underlying the formation of innate immune memory. Finally, we explore the health implications together with the potential therapeutic interventions harnessing trained immunity.
    Keywords:  Cellular signaling; Epigenetics; Immune memory; Metabolism; Trained immunity
  3. J Leukoc Biol. 2023 Jun 29. pii: qiad070. [Epub ahead of print]
      The early immune response to bacterial pneumonia requires a careful balance between pathogen clearance and tissue damage. The anti-inflammatory cytokine IL-10 is critical for restraining otherwise lethal pulmonary inflammation. However, pathogen-induced IL-10 is associated with bacterial persistence in the lungs. In this study, we used mice with myeloid cell specific deletion of IL-10R to investigate the cellular targets of IL-10 immune suppression during infection with Streptococcus pneumoniae, the most common bacterial cause of pneumonia. Our findings suggest that IL-10 restricts the neutrophil response to S. pneumoniae, as neutrophil recruitment to the lungs was elevated in myeloid IL-10R deficient mice and neutrophils in the lungs of these mice were more effective at killing S. pneumoniae. Improved killing of S. pneumoniae was associated with increased production of reactive oxygen species (ROS) and serine protease activity in IL-10R deficient neutrophils. Similarly, IL-10 suppressed the ability of human neutrophils to kill S. pneumoniae. Burdens of S. pneumoniae were lower in myeloid IL-10R deficient mice compared with wild-type mice, and adoptive transfer of IL-10R deficient neutrophils into wild-type mice significantly improved pathogen clearance. Despite the potential for neutrophils to contribute to tissue damage, lung pathology scores were similar between genotypes. This contrasts with total IL-10 deficiency, which is associated with increased immunopathology during S. pneumoniae infection. Together, these findings identify neutrophils as a critical target of S. pneumoniae-induced immune suppression and highlight myeloid IL-10R abrogation as a mechanism to selectively reduce pathogen burdens without exacerbating pulmonary damage.
    Keywords:   Streptococcus pneumoniae ; IL-10; IL-10R; Neutrophils; anti-inflammatory; cytokines; host-pathogen interactions; immune evasion; lung infection; myeloid cells; pneumonia; pulmonary
  4. Methods Mol Biol. 2023 ;2692 1-13
      Herein, we provide a colony forming unit (CFU)-based counting method for quantitating the bacterial binding, phagocytosis, and killing capacity of phagocytes. Although these functions can be measured by immunofluorescence- and dye-based assays, quantitating CFUs are comparatively inexpensive and easy to perform. The protocol described below is easily modified for use with different phagocytes (e.g., macrophages, neutrophils, cell lines), types of bacteria, or opsonic conditions.
    Keywords:  Bacterial killing; Gentamicin protection; Macrophage; Particle binding; Phagocyte; Phagocytosis
  5. Exp Dermatol. 2023 Jun 30.
      Dermal fibroblasts are the main resident cells of the dermis. They have several significant functions related to wound healing, extracellular matrix production and hair cycling. Dermal fibroblasts can also act as sentinels in defence against infection. They express pattern recognition receptors such as toll-like receptors to sense pathogen components, followed by the synthesis of pro-inflammatory cytokines (including IL-6, IFN-β and TNF-α), chemokines (such as IL-8 and CXCL1) and antimicrobial peptides. Dermal fibroblasts also secrete other molecules-like growth factors and matrix metalloproteinases to benefit tissue repair from infection. Crosstalk between dermal fibroblasts and immune cells may amplify the immune response against infection. Moreover, the transition of a certain adipogenic fibroblasts to adipocytes protects skin from bacterial infection. Together, we discuss the role of dermal fibroblasts in the war against pathogens in this review. Dermal fibroblasts have important immune functions in anti-infection immunity, which should not be overlooked.
    Keywords:  dermal fibroblasts; infection; innate immune; skin
  6. Biomedicines. 2023 May 24. pii: 1521. [Epub ahead of print]11(6):
      Immune responses are highly complex and intricately regulated processes involving immune and non-immune cells in close direct and indirect contact with each other. These cells are highly sensitive to environmental signals, including factors derived from microbiota. Here, we demonstrate that the human microbiota member Lactobacillus casei (L. casei)-derived cell-free supernatant (CFS) enhances the sensitivity of mesenchymal-stromal-cell-like (MSCI) cells to viral stimuli and induces the development of dendritic cells (DCs) with anti-inflammatory and antiviral properties via pretreated MSCl cells. Our results showed that the production of INFβ and CXCL10 by MSCl cells upon viral stimulation was dependent on the presence of L. casei-derived extracellular vesicles in CFS during pretreatment. Moreover, L. casei CFS and/or poly (I:C)-conditioned MSCI cells altered the differentiation process of freshly isolated monocytes, as well as the developing DCs' phenotype and functional activities, such as cytokine and chemokine secretion. Taken together, L. casei CFS contains factors which contribute to the pronounced antiviral response of MSCI cells, avoiding the development of inflammation via the induction of differentiation of anti-inflammatory DCs that retain their antiviral properties.
    Keywords:  Lactobacillus; dendritic cells; extracellular vesicles; immunomodulation; mesenchymal stromal cells
  7. Semin Immunol. 2023 Jun 26. pii: S1044-5323(23)00086-6. [Epub ahead of print]69 101795
      The rapid rise in atopy and asthma in industrialized nations has led to the identification of early life environmental factors that promote these conditions and spurred research into how such exposures may mediate the trajectory to childhood disease development. Over the past decade, the human microbiome has emerged as a key determinant of human health. This is largely due to the increasing appreciation for the myriad of non-mutually exclusive mechanisms by which microbes tune and train host immunity. Microbiomes, particularly those in early life, are shaped by extrinsic and intrinsic factors, including many of the exposures known to influence allergy and asthma risk. This has led to the over-arching hypothesis that such exposures mediate their effect on childhood atopy and asthma by altering the functions and metabolic productivity of microbiomes that shape immune function during this critical developmental period. The capacity to study microbiomes at the genetic and molecular level in humans from the pre-natal period into childhood with well-defined clinical outcomes, offers an unprecedented opportunity to identify early-life and inter-generational determinants of atopy and asthma outcomes. Moreover, such studies provide an integrative microbiome research framework that can be applied to other chronic inflammatory conditions. This review attempts to capture key studies in the field that offer insights into the developmental origins of childhood atopy and asthma, providing novel insights into microbial mediators of maladaptive immunity and chronic inflammatory disease in childhood.
    Keywords:  Asthma; Atopy; Immunity; Microbiome
  8. Mucosal Immunol. 2023 Jun 27. pii: S1933-0219(23)00051-X. [Epub ahead of print]
      Macrophages play essential roles in tissue homeostasis, defence, and repair. Their functions are highly tissue-specific and, when damage and inflammation stimulate repopulation by circulating monocytes, the incoming monocytes rapidly acquire the same, tissue-specific functions as the previous, resident macrophages. Several environmental factors are thought to guide the functional differentiation of recruited monocytes, including metabolic pressures imposed by the fuel sources available in each tissue. Here we discuss whether such a model of metabolic determinism can be applied to macrophage differentiation across barrier sites, from the lung to the skin. We suggest an alternative model, in which metabolic phenotype is a consequence of macrophage longevity rather than an early driver of tissue-specific adaption.
  9. Gut Microbes. 2023 Jan-Dec;15(1):15(1): 2226916
      A diverse array of commensal microorganisms inhabits the human intestinal tract. The most abundant and most studied members of this microbial community are undoubtedly bacteria. Their important role in gut physiology, defense against pathogens, and immune system education has been well documented over the last decades. However, the gut microbiome is not restricted to bacteria. It encompasses the entire breadth of microbial life: viruses, archaea, fungi, protists, and parasitic worms can also be found in the gut. While less studied than bacteria, their divergent but important roles during health and disease have become increasingly more appreciated. This review focuses on these understudied members of the gut microbiome. We will detail the composition and development of these microbial communities and will specifically highlight their functional interactions with enteric pathogens, such as species of the family Enterobacteriaceae. The interactions can be direct through physical interactions, or indirect through secreted metabolites or modulation of the immune response. We will present general concepts and specific examples of how non-bacterial gut communities modulate bacterial pathogenesis and present an outlook for future gut microbiome research that includes these communities.
    Keywords:  Enterobacteriaceae; Microbiota; archaea; enteric pathogens; fungi; gut; microbiome; parasites; viruses
  10. Front Immunol. 2023 ;14 1195988
      Pulmonary alveolar proteinosis (PAP) is a rare pulmonary disorder that is characterized by the abnormal accumulation of surfactant within the alveoli. Alveolar macrophages (AMs) have been identified as playing a pivotal role in the pathogenesis of PAP. In most of PAP cases, the disease is triggered by impaired cholesterol clearance in AMs that depend on granulocyte-macrophage colony-stimulating factor (GM-CSF), resulting in defective alveolar surfactant clearance and disruption of pulmonary homeostasis. Currently, novel pathogenesis-based therapies are being developed that target the GM-CSF signaling, cholesterol homeostasis, and immune modulation of AMs. In this review, we summarize the origin and functional role of AMs in PAP, as well as the latest therapeutic strategies aimed at addressing this disease. Our goal is to provide new perspectives and insights into the pathogenesis of PAP, and thereby identify promising new treatments for this disease.
    Keywords:  alveolar macrophage (AM); granulocyte-macrophage colony-stimulating factor (GM-CSF); pulmonary alveolar proteinosis (PAP); pulmonary homeostasis; therapeutic strategies
  11. Cells. 2023 06 13. pii: 1615. [Epub ahead of print]12(12):
      Metabolic and immune cell responses are intimately linked and cross-regulated [...].
  12. J Bacteriol. 2023 Jun 29. e0012723
      Techniques by which to genetically manipulate members of the microbiota enable both the evaluation of host-microbe interactions and an avenue by which to monitor and modulate human physiology. Genetic engineering applications have traditionally focused on model gut residents, such as Escherichia coli and lactic acid bacteria. However, emerging efforts by which to develop synthetic biology toolsets for "nonmodel" resident gut microbes could provide an improved foundation for microbiome engineering. As genome engineering tools come online, so too have novel applications for engineered gut microbes. Engineered resident gut bacteria facilitate investigations of the roles of microbes and their metabolites on host health and allow for potential live microbial biotherapeutics. Due to the rapid pace of discovery in this burgeoning field, this minireview highlights advancements in the genetic engineering of all resident gut microbes.
    Keywords:  CRISPR-Cas; metabolic engineering; microbiome; nonmodel organisms; synthetic biology
  13. Pathogens. 2023 May 26. pii: 765. [Epub ahead of print]12(6):
      Staphylococcus aureus is both a human commensal and a pathogen, that causes serious nosocomial and community-acquired infections. Despite nostrils being considered its preferred host habitat, the oral cavity has been demonstrated to be an ideal starting point for auto-infection and transmission. The antibiotic resistance assessment of S. aureus is a priority and is often reported in clinical settings. This study aimed to explore the prevalence and antimicrobial susceptibility of S. aureus in the oral and nasal cavities of healthy individuals. The participants (n = 101) were subjected to a demographic and clinical background survey, a caries evaluation, and to oral and nasal swabbing. Swabs were cultured in differential/selective media and S. aureus isolates were identified (MALDI-TOF MS) and tested for antibiotic susceptibility (EUCAST/CLSI). Similar S. aureus prevalence was found exclusively on nasal (13.9%) or oral (12.0%) habitats, whereas 9.9% of the population were simultaneous nasal and oral carriers. In oro-nasal cavities, similar antibiotic resistance rates (83.3-81.5%), including MDR (20.8-29.6%), were observed. Notably, 60% (6/10) of the simultaneous nasal and oral carriers exhibited different antibiotic resistance profiles between cavities. This study demonstrates the relevance of the oral cavity as an independent colonization site for S. aureus and as a potential source of antimicrobial resistance, a role which has been widely neglected so far.
    Keywords:  Staphylococcus aureus; antibiotic resistance; healthy individuals; multidrug-resistance; oro-nasal carriage
  14. Front Immunol. 2023 ;14 1233791
    Keywords:  adipose tissue macrophages; innate immunity; metabolic diseases; metabolism; obesity; phenotype; plasticity; therapeutic target
  15. Front Nutr. 2023 ;10 1168582
      Introduction: Dysbiosis of the gut microbiome may augment lung disease via the gut-lung axis. Proteobacteria may contribute to tissue proteolysis followed by neutrophil recruitment, lung tissue injury, and perpetuation of chronic inflammation. To study the effects of probiotics across the gut-lung axis, we sought to determine if a Lactobacillus probiotic and herbal blend was safe and well-tolerated in healthy volunteers and asthmatic patients.Methods: We conducted a 1-month randomized, open-label clinical trial in Cork, Ireland with healthy and asthmatic patients who took the blend twice a day. The primary endpoint was safety with exploratory endpoints including quality of life, lung function, gut microbiome ecology, and inflammatory biomarkers.
    Results: All subjects tolerated the blend without adverse events. Asthmatic subjects who took the blend showed significant improvements in lung function as measured by forced expiratory volume and serum short chain fatty acid levels from baseline to Week 4. The gut microbiome of asthmatic subjects differed significantly from controls, with the most prominent difference in the relative abundance of the proteobacteria Escherichia coli. Administration of the probiotic maintained overall microbial community architecture with the only significant difference being an increase in absolute abundance of the probiotic strains measured by strain-specific PCR.
    Conclusion: This study supports the safety and efficacy potential of a Lactobacillus probiotic plus herbal blend to act on the gut-lung axis. However, due to the lack of a control group, a longer blinded, placebo-controlled study will be warranted to confirm the efficacy improvements observed in this trial.
    Clinical trial registration:, identifier NCT05173168.
    Keywords:  Lactobacillus; asthma; gut-lung axis; microbiome; probiotic; short-chain fatty acids
  16. Children (Basel). 2023 Jun 05. pii: 1020. [Epub ahead of print]10(6):
      Esophageal atresia (EA) is a rare birth defect in which respiratory tract disorders are a major cause of morbidity. It remains unclear whether respiratory tract disorders are in part caused by alterations in airway epithelial cell functions such as the activity of motile cilia. This can be studied using airway epithelial cell culture models of patients with EA. Therefore, the aim of this study was to evaluate the feasibility to culture and functionally characterize motile cilia function in the differentiated air-liquid interface cultured airway epithelial cells and 3D organoids derived from nasal brushings and bronchoalveolar lavage (BAL) fluid from children with EA. We demonstrate the feasibility of culturing differentiated airway epithelia and organoids of nasal brushings and BAL fluid of children with EA, which display normal motile cilia function. EA patient-derived airway epithelial cultures can be further used to examine whether alterations in epithelial functions contribute to respiratory disorders in EA.
    Keywords:  airway epithelium; esophageal atresia; organoids; primary ciliary dyskinesia; tracheal anomaly
  17. Sci Signal. 2023 06 27. 16(791): eadj3337
      Host reactive nitrogen species maintain intracellular Salmonella in an antibiotic-tolerant, persister state.
  18. mSphere. 2023 Jun 26. e0012223
      The contributions of commensal fungi to human health and disease are not well understood. Candida species such as C. albicans and C. glabrata are opportunistic pathogenic fungi and common colonizers of the human intestinal tract. They have been shown to affect the host immune system and interact with the gut microbiome and pathogenic microorganisms. Therefore, Candida species could be expected to play important ecological roles in the host gastrointestinal tract. Previously, our group demonstrated that pre-colonization of mice with C. albicans protected them against lethal C. difficile infection (CDI). Here, we show that mice pre-colonized with C. glabrata succumbed to CDI more rapidly than mice that were not pre-colonized suggesting an enhancement in C. difficile pathogenesis. Further, when C. difficile was added to pre-formed C. glabrata biofilms, an increase in matrix and overall biomass was observed. These effects were also shown with C. glabrata clinical isolates. Interestingly, the presence of C. difficile increased C. glabrata biofilm susceptibility to caspofungin, indicating potential effects on the fungal cell wall. Defining this intricate and intimate relationship will lead to an understanding of the role of Candida species in the context of CDI and novel aspects of Candida biology. IMPORTANCE Most microbiome studies have only considered the bacterial populations while ignoring other members of the microbiome such as fungi, other eukaryotic microorganisms, and viruses. Therefore, the role of fungi in human health and disease has been significantly understudied compared to their bacterial counterparts. This has generated a significant gap in knowledge that has negatively impacted disease diagnosis, understanding, and the development of therapeutics. With the development of novel technologies, we now have an understanding of mycobiome composition, but we do not understand the roles of fungi in the host. Here, we present findings showing that Candida glabrata, an opportunistic pathogenic yeast that colonizes the mammalian gastrointestinal tract, can impact the severity and outcome of a Clostridioides difficile infection (CDI) in a murine model. These findings bring attention to fungal colonizers during CDI, a bacterial infection of the gastrointestinal tract.
    Keywords:  Candida glabrata; Clostridioides difficile; biofilms; colonization; gastrointestinal infections; polymicrobial interactions
  19. Sci Signal. 2023 06 27. 16(791): eabm9454
      Dendritic cells (DCs) that express T cell immunoglobulin domain molecule-4 (TIM4), a cell surface receptor for phosphatidylserine, induce T helper 2 (TH2) cell responses and allergic reactions. We elucidated the role of the transcription factor X-box-binding protein-1 (XBP1) in the induction of the TH2 cell response through its role in generating TIM4+ DCs. We found that XBP1 was required for TIM4 mRNA and protein expression in airway DCs in response to the cytokine interleukin-2 (IL-2) and that this pathway was required for TIM4 expression on DCs in response to the allergens PM2.5 and Derf1. The IL-2-XBP1-TIM4 axis in DCs contributed to Derf1/PM2.5-induced, aberrant TH2 cell responses in vivo. An interaction between the guanine nucleotide exchange factor Son of sevenless-1 (SOS1) and the GTPase RAS promoted XBP1 and TIM4 production in DCs. Targeting the XBP1-TIM4 pathway in DCs prevented or alleviated experimental airway allergy. Together, these data suggest that XBP1 is required for TH2 cell responses by inducing the development of TIM4+ DCs, which depends on the IL-2-XBP1-SOS1 axis. This signaling pathway provides potential therapeutic targets for the treatment of TH2 cell-dependent inflammation or allergic diseases.
  20. Biomolecules. 2023 06 06. pii: 945. [Epub ahead of print]13(6):
      Wound healing is triggered by inflammation elicited after tissue injury. Mesenchymal cells, specifically fibroblasts, accumulate in the injured tissues, where they engage in tissue repair through the expression and assembly of extracellular matrices that provide a scaffold for cell adhesion, the re-epithelialization of tissues, the production of soluble bioactive mediators that promote cellular recruitment and differentiation, and the regulation of immune responses. If appropriately deployed, these processes promote adaptive repair, resulting in the preservation of the tissue structure and function. Conversely, the dysregulation of these processes leads to maladaptive repair or disrepair, which causes tissue destruction and a loss of organ function. Thus, fibroblasts not only serve as structural cells that maintain tissue integrity, but are key effector cells in the process of wound healing. The review will discuss the general concepts about the origins and heterogeneity of this cell population and highlight the specific fibroblast functions disrupted in human disease. Finally, the review will explore the role of fibroblasts in tissue disrepair, with special attention to the lung, the role of aging, and how alterations in the fibroblast phenotype underpin disorders characterized by pulmonary fibrosis.
    Keywords:  extracellular matrix; fibroblasts; fibrosis; integrins
  21. Eur J Immunol. 2023 Jun 27. e2250307
      Type I IFNs are critical for host responses to viral infection and are also implicated in the pathogenesis of multiple autoimmune diseases. Multiple subtypes exist within the type I IFN family, in particular 13 distinct IFN-α genes, which signal through the same heterodimer receptor that is ubiquitously expressed by mammalian cells. Both evolutionary genetic studies and functional antiviral assays strongly suggest differential functions and activity between the 13 IFN-α subtypes, yet we still lack a clear understanding of these different roles. This review summarizes the evidence from studies describing differential functions of IFN-α subtypes and highlights potential reasons for discrepancies between the reports. We examine both acute and chronic viral infection, as well as autoimmunity, and integrate a more recent awareness of the importance of anti-IFN-α autoantibodies in shaping the type I IFN responses in these different conditions.
    Keywords:  Autoantibodies; Autoimmunity; IFN-α, Infection; Type I IFNs
  22. bioRxiv. 2023 Apr 28. pii: 2023.04.26.538482. [Epub ahead of print]
      The appropriate development of macrophages, the body's professional phagocyte, is essential for organismal development, especially in mammals. This dependence is exemplified by the observation that loss-of-function mutations in colony stimulating factor 1 receptor (CSF1R) results in multiple tissue abnormalities owing to an absence of macrophages. Despite this importance, little is known about the molecular and cell biological regulation of macrophage development. Here, we report the surprising finding that the chloride-sensing kinase With-no-lysine 1 (WNK1) is required for development of tissue-resident macrophages (TRMs). Myeloid-specific deletion of Wnk1 resulted in a dramatic loss of TRMs, disrupted organ development, systemic neutrophilia, and mortality between 3 and 4 weeks of age. Strikingly, we found that myeloid progenitors or precursors lacking WNK1 not only failed to differentiate into macrophages, but instead differentiated into neutrophils. Mechanistically, the cognate CSF1R cytokine macrophage-colony stimulating factor (M-CSF) stimulates macropinocytosis by both mouse and human myeloid progenitors and precursor cells. Macropinocytosis, in turn, induces chloride flux and WNK1 phosphorylation. Importantly, blocking macropinocytosis, perturbing chloride flux during macropinocytosis, and inhibiting WNK1 chloride-sensing activity each skewed myeloid progenitor differentiation from macrophages into neutrophils. Thus, we have elucidated a role for WNK1 during macropinocytosis and discovered a novel function of macropinocytosis in myeloid progenitors and precursor cells to ensure macrophage lineage fidelity.Highlights: Myeloid-specific WNK1 loss causes failed macrophage development and premature deathM-CSF-stimulated myeloid progenitors and precursors become neutrophils instead of macrophagesM-CSF induces macropinocytosis by myeloid progenitors, which depends on WNK1Macropinocytosis enforces macrophage lineage commitment.
  23. Pediatr Allergy Immunol. 2023 06;34(6): e13976
      The homogeneous impact of local dysbiosis on the development of allergic diseases in the same organ has been thoroughly studied. However, much less is known about the heterogeneous influence of dysbiosis within one organ on allergic diseases in other organs. A comprehensive analysis of the current scientific literature revealed that most of the relevant publications focus on only three organs: gut, airways, and skin. Moreover, the interactions appear to be mainly unidirectional, that is, dysbiotic conditions of the gut being associated with allergic diseases of the airways and the skin. Similar to homogeneous interactions, early life appears to be not only a crucial period for the formation of the microbiota in one organ but also for the later development of allergic diseases in other organs. In particular, we were able to identify a number of specific bacterial and fungal species/genera in the intestine that were repeatedly associated in the literature with either increased or decreased allergic diseases of the skin, like atopic dermatitis, or the airways, like allergic rhinitis and asthma. The reported studies indicate that in addition to the composition of the microbiome, also the relative abundance of certain microbial species and the overall diversity are associated with allergic diseases of the corresponding organs. As anticipated for human association studies, the underlying mechanisms of the organ-organ crosstalk could not be clearly resolved yet. Thus, further work, in particular experimental animal studies are required to elucidate the mechanisms linking dysbiotic conditions of one organ to allergic diseases in other organs.
    Keywords:  allergy; asthma; atopic dermatitis; dysbiosis; heterogeneous organ-organ interactions; human microbiota
  24. Biomedicines. 2023 May 30. pii: 1582. [Epub ahead of print]11(6):
      Autoimmune (AI) diseases, which present in a multitude of systemic manifestations, have been connected to many underlying factors. These factors include the environment, genetics, individual microbiomes, and diet. An individual's gut microbiota is an integral aspect of human functioning, as it is intimately integrated into the metabolic, mechanical, immunological, and neurologic pathways of the body. The microbiota dynamically changes throughout our lifetimes and is individually unique. While the gut microbiome is ever-adaptive, gut dysbiosis can exert a significant influence on physical and mental health. Gut dysbiosis is a common factor in various AI, and diets with elevated fat and sugar content have been linked to gut microbiome alterations, contributing to increased systemic inflammation. Additionally, multiple AI's have increased levels of certain inflammatory markers such as TNF-a, IL-6, and IL-17 that have been shown to contribute to arthropathy and are also linked to increased levels of gut dysbiosis. While chronic inflammation has been shown to affect many physiologic systems, this review explores the connection between gut microbiota, bone metabolism, and the skeletal and joint destruction associated with various AI, including psoriatic arthritis, systemic lupus erythematosus, irritable bowel disease, and rheumatoid arthritis. This review aims to define the mechanisms of microbiome crosstalk between the cells of bone and cartilage, as well as to investigate the potential bidirectional connections between AI, bony and cartilaginous tissue, and the gut microbiome. By doing this, the review also introduces the concept of altering an individual's specific gut microbiota as a form of regenerative medicine and potential tailored therapy for joint destruction seen in AI. We hope to show multiple, specific ways to target the microbiome through diet changes, rebalancing microbial diversity, or decreasing specific microbes associated with increased gut permeability, leading to reduced systemic inflammation contributing to joint pathology. Additionally, we plan to show that diet alterations can promote beneficial changes in the gut microbiota, supporting the body's own endogenous processes to decrease inflammation and increase healing. This concept of microbial alteration falls under the definition of regenerative medicine and should be included accordingly. By implementing microbial alterations in regenerative medicine, this current study could lend increasing support to the current research on the associations of the gut microbiota, bone metabolism, and AI-related musculoskeletal pathology.
    Keywords:  arthropathy; autoimmune; bone metabolism; gut dysbiosis; microbiome; regenerative medicine
  25. Free Radic Biol Med. 2023 Jun 23. pii: S0891-5849(23)00508-7. [Epub ahead of print]
      Myeloperoxidase (MPO) is released by neutrophils in inflamed tissues. MPO oxidizes chloride, bromide, and thiocyanate to produce hypochlorous acid (HOCl), hypobromous acid (HOBr), and hypothiocyanous acid (HOSCN), respectively. These oxidants are toxic to pathogens, but may also react with host cells to elicit biological activity and potential toxicity. In cystic fibrosis (CF) and related diseases, increased neutrophil inflammation leads to increased airway MPO and airway epithelial cell (AEC) exposure to its oxidants. In this study, we investigated how equal dose-rate exposures of MPO-derived oxidants differentially impact the metabolome of human AECs (BEAS-2B cells). We utilized enzymatic oxidant production with rate-limiting glucose oxidase (GOX) coupled to MPO, and chloride, bromide (Br-), or thiocyanate (SCN-) as substrates. AECs exposed to GOX/MPO/SCN- (favoring HOSCN) were viable after 24 h, while exposure to GOX/MPO (favoring HOCl) or GOX/MPO/Br- (favoring HOBr) developed cytotoxicity after 6 h. Cell glutathione and peroxiredoxin-3 oxidation were insufficient to explain these differences. However, untargeted metabolomics revealed GOX/MPO and GOX/MPO/Br- diverged significantly from GOX/MPO/SCN- for dozens of metabolites. We noted methionine sulfoxide and dehydromethionine were significantly increased in GOX/MPO- or GOX/MPO/Br--treated cells, and analyzed them as potential biomarkers of lung damage in bronchoalveolar lavage fluid from 5-year-olds with CF (n = 27). Both metabolites were associated with increasing bronchiectasis, neutrophils, and MPO activity. This suggests MPO production of HOCl and/or HOBr may contribute to inflammatory lung damage in early CF. In summary, our in vitro model enabled unbiased identification of exposure-specific metabolite products which may serve as biomarkers of lung damage in vivo. Continued research with this exposure model may yield additional oxidant-specific biomarkers and reveal explicit mechanisms of oxidant byproduct formation and cellular redox signaling.
    Keywords:  Cystic fibrosis; Dehydromethionine; Hypothiocyanite; Metabolomics; Myeloperoxidase; Oxidative stress
  26. Biochip J. 2023 May 22. 1-27
      In vitro model systems have been advanced to recapitulate important physiological features of the target organ in vivo more closely than the conventional cell line cultures on a petri dish. The advanced organotypic model systems can be used as a complementary or alternative tool for various testing and screening. Numerous data from germ-free animal studies and genome sequencings of clinical samples indicate that human microbiota is an essential part of the human body, but current in vitro model systems rarely include them, which can be one of the reasons for the discrepancy in the tissue phenotypes and outcome of therapeutic intervention between in vivo and in vitro tissues. A coculture model system with appropriate microbes and host cells may have great potential to bridge the gap between the in vitro model and the in vivo counterpart. However, successfully integrating two species in one system introduces new variables to consider and poses new challenges to overcome. This review aims to provide perspectives on the important factors that should be considered for developing organotypic bacterial coculture models. Recent advances in various organotypic bacterial coculture models are highlighted. Finally, challenges and opportunities in developing organotypic microbial coculture models are also discussed.
    Keywords:  Bacterial coculture; Commensal bacteria; Microphysiological systems; Organotypic model systems
  27. mSystems. 2023 Jun 30. e0126522
      The ability of bacterial pathogens to metabolically adapt to the environmental conditions of their hosts is critical to both colonization and invasive disease. Infection with Neisseria gonorrhoeae (the gonococcus, Gc) is characterized by the influx of neutrophils [polymorphonuclear leukocytes (PMNs)], which fail to clear the bacteria and make antimicrobial products that can exacerbate tissue damage. The inability of the human host to clear Gc infection is particularly concerning in light of the emergence of strains that are resistant to all clinically recommended antibiotics. Bacterial metabolism represents a promising target for the development of new therapeutics against Gc. Here, we generated a curated genome-scale metabolic network reconstruction (GENRE) of Gc strain FA1090. This GENRE links genetic information to metabolic phenotypes and predicts Gc biomass synthesis and energy consumption. We validated this model with published data and in new results reported here. Contextualization of this model using the transcriptional profile of Gc exposed to PMNs revealed substantial rearrangements of Gc central metabolism and induction of Gc nutrient acquisition strategies for alternate carbon source use. These features enhanced the growth of Gc in the presence of neutrophils. From these results, we conclude that the metabolic interplay between Gc and PMNs helps define infection outcomes. The use of transcriptional profiling and metabolic modeling to reveal new mechanisms by which Gc persists in the presence of PMNs uncovers unique aspects of metabolism in this fastidious bacterium, which could be targeted to block infection and thereby reduce the burden of gonorrhea in the human population. IMPORTANCE The World Health Organization designated Gc as a high-priority pathogen for research and development of new antimicrobials. Bacterial metabolism is a promising target for new antimicrobials, as metabolic enzymes are widely conserved among bacterial strains and are critical for nutrient acquisition and survival within the human host. Here we used genome-scale metabolic modeling to characterize the core metabolic pathways of this fastidious bacterium and to uncover the pathways used by Gc during culture with primary human immune cells. These analyses revealed that Gc relies on different metabolic pathways during co-culture with human neutrophils than in rich media. Conditionally essential genes emerging from these analyses were validated experimentally. These results show that metabolic adaptation in the context of innate immunity is important to Gc pathogenesis. Identifying the metabolic pathways used by Gc during infection can highlight new therapeutic targets for drug-resistant gonorrhea.
    Keywords:  Neisseria gonorrhoeae; carbon metabolism; genome-scale metabolic network reconstruction; metabolic network analysis; metabolism; neutrophils; transcriptomics
  28. Microorganisms. 2023 Jun 02. pii: 1484. [Epub ahead of print]11(6):
      Human skin and its commensal microbiome form the first layer of protection to the outside world. A dynamic microbial ecosystem of bacteria, fungi and viruses, with the potential to respond to external insult, the skin microbiome has been shown to evolve over the life course with an alteration in taxonomic composition responding to altered microenvironmental conditions on human skin. This work sought to investigate the taxonomic, diversity and functional differences between infant and adult leg skin microbiomes. A 16S rRNA gene-based metataxonomic analysis revealed significant differences between the infant and adult skin groups, highlighting differential microbiome profiles at both the genus and species level. Diversity analysis reveals differences in the overall community structure and associated differential predicted functional profiles between the infant and adult skin microbiome suggest differing metabolic processes are present between the groups. These data add to the available information on the dynamic nature of skin microbiome during the life course and highlight the predicted differential microbial metabolic process that exists on infant and adult skin, which may have an impact on the future design and use of cosmetic products that are produced to work in consort with the skin microbiome.
    Keywords:  adult; function; infant; microbiome; networks; skin
  29. Elife. 2023 Jun 30. pii: RP87192. [Epub ahead of print]12
      The skin microbiome provides vital contributions to human health. However, the spatial organization and viability of its bacterial components remain unclear. Here, we apply culturing, imaging, and molecular approaches to human and mouse skin samples, and find that the skin surface is colonized by fewer viable bacteria than predicted by bacterial DNA levels. Instead, viable skin-associated bacteria are predominantly located in hair follicles and other cutaneous invaginations. Furthermore, we show that the skin microbiome has a uniquely low fraction of viable bacteria compared to other human microbiome sites, indicating that most bacterial DNA on the skin surface is not associated with viable cells Additionally, a small number of bacterial families dominate each skin site and traditional sequencing methods overestimate both the richness and diversity of the skin microbiome. Finally, we performed an in vivo skin microbiome perturbation-recovery study using human volunteers. Bacterial 16S rRNA gene sequencing revealed that, while the skin microbiome is remarkably stable even in the wake of aggressive perturbation, repopulation of the skin surface is driven by the underlying viable population. Our findings help explain the dynamics of skin microbiome perturbation as bacterial DNA on the skin surface can be transiently perturbed but is replenished by a stable underlying viable population. These results address multiple outstanding questions in skin microbiome biology with significant implications for future efforts to study and manipulate it.
    Keywords:  Cutibacterium acnes; E. coli; Staphylococcus epidermidis; bacterial viability; human; infectious disease; microbiology; microbiome
  30. Int J Mol Sci. 2023 Jun 10. pii: 9994. [Epub ahead of print]24(12):
      Sialic acids (SAs) are α-keto-acid sugars with a nine-carbon backbone present at the non-reducing end of human milk oligosaccharides and the glycan moiety of glycoconjugates. SAs displayed on cell surfaces participate in the regulation of many physiologically important cellular and molecular processes, including signaling and adhesion. Additionally, sialyl-oligosaccharides from human milk act as prebiotics in the colon by promoting the settling and proliferation of specific bacteria with SA metabolism capabilities. Sialidases are glycosyl hydrolases that release α-2,3-, α-2,6- and α-2,8-glycosidic linkages of terminal SA residues from oligosaccharides, glycoproteins and glycolipids. The research on sialidases has been traditionally focused on pathogenic microorganisms, where these enzymes are considered virulence factors. There is now a growing interest in sialidases from commensal and probiotic bacteria and their potential transglycosylation activity for the production of functional mimics of human milk oligosaccharides to complement infant formulas. This review provides an overview of exo-alpha-sialidases of bacteria present in the human gastrointestinal tract and some insights into their biological role and biotechnological applications.
    Keywords:  formula milk; human milk; human milk oligosaccharides; neuraminidase; sialic acid; sialidase
  31. Trends Genet. 2023 Jun 24. pii: S0168-9525(23)00127-0. [Epub ahead of print]
      Metatranscriptomics refers to the analysis of the collective microbial transcriptome of a sample. Its increased utilization for the characterization of human-associated microbial communities has enabled the discovery of many disease-state related microbial activities. Here, we review the principles of metatranscriptomics-based analysis of human-associated microbial samples. We describe strengths and weaknesses of popular sample preparation, sequencing, and bioinformatics approaches and summarize strategies for their use. We then discuss how human-associated microbial communities have recently been examined and how their characterization may change. We conclude that metatranscriptomics insights into human microbiotas under health and disease have not only expanded our knowledge on human health, but also opened avenues for rational antimicrobial drug use and disease management.
    Keywords:  RNA-sequencing; functional and taxonomic annotation; human microbiota; metatranscriptome; metatranscriptomics; sample preparation
  32. Microorganisms. 2023 May 31. pii: 1453. [Epub ahead of print]11(6):
      The oral microbiome is a complex and dynamic assemblage of microorganisms that normally exist within the mouth, contributing to host health via a number of mechanisms, including exclusion of harmful microbes and immune optimization [...].
  33. Gut Microbes. 2023 Jan-Dec;15(1):15(1): 2222961
      L-arginine (L-arg) is a versatile amino acid and a central intestinal metabolite in mammalian and microbial organisms. Thus, L-arg participates as precursor of multiple metabolic pathways in the regulation of cell division and growth. It also serves as a source of carbon, nitrogen, and energy or as a substrate for protein synthesis. Consequently, L-arg can simultaneously modify mammalian immune functions, intraluminal metabolism, intestinal microbiota, and microbial pathogenesis. While dietary intake, protein turnover or de novo synthesis usually supply L-arg in sufficient amounts, the expression of several key enzymes of L-arg metabolism can change rapidly and dramatically following inflammation, sepsis, or injury. Consequently, the availability of L-arg can be restricted due to increased catabolism, transforming L-arg into an essential amino acid. Here, we review the enzymatic pathways of L-arg metabolism in microbial and mammalian cells and their role in immune function, intraluminal metabolism, colonization resistance, and microbial pathogenesis in the gut.
    Keywords:  L-arginine (L-arg); colonization resistance; dietary L-arg supplementation; host–microbe interaction; intestinal microbiota; microbial pathogenesis; mucosal immune function; mutual metabolic pathways; virulence factor
  34. Pharmaceutics. 2023 May 29. pii: 1615. [Epub ahead of print]15(6):
      β-glucan, one of the homopolysaccharides composed of D-glucose, exists widely in cereals and microorganisms and possesses various biological activities, including anti-inflammatory, antioxidant, and anti-tumor properties. More recently, there has been mounting proof that β-glucan functions as a physiologically active "biological response modulator (BRM)", promoting dendritic cell maturation, cytokine secretion, and regulating adaptive immune responses-all of which are directly connected with β-glucan-regulated glucan receptors. This review focuses on the sources, structures, immune regulation, and receptor recognition mechanisms of β-glucan.
    Keywords:  adjuvants; dendritic cells; immune system; β-glucans
  35. Front Cell Infect Microbiol. 2023 ;13 1194254
      Background: Atopic dermatitis (AD) is a chronic inflammatory skin condition whose pathogenesis involves genetic predisposition, epidermal barrier dysfunction, alterations in the immune responses and microbial dysbiosis. Clinical studies have shown a link between Staphylococcus aureus and the pathogenesis of AD, although the origins and genetic diversity of S. aureus colonizing patients with AD is poorly understood. The aim of the study was to investigate if specific clones might be associated with the disease.Methods: WGS analyses were performed on 38 S. aureus strains, deriving from AD patients and healthy carriers. Genotypes (i.e. MLST, spa-, agr- and SCCmec-typing), genomic content (e.g. virulome and resistome), and the pan-genome structure of strains have been investigated. Phenotypic analyses were performed to determine the antibiotic susceptibility, the biofilm production and the invasiveness within the investigated S. aureus population.
    Results: Strains isolated from AD patients revealed a high degree of genetic heterogeneity and a shared set of virulence factors and antimicrobial resistance genes, suggesting that no genotype and genomic content are uniquely associated with AD. The same strains were characterized by a lower variability in terms of gene content, indicating that the inflammatory conditions could exert a selective pressure leading to the optimization of the gene repertoire. Furthermore, genes related to specific mechanisms, like post-translational modification, protein turnover and chaperones as well as intracellular trafficking, secretion and vesicular transport, were significantly more enriched in AD strains. Phenotypic analysis revealed that all of our AD strains were strong or moderate biofilm producers, while less than half showed invasive capabilities.
    Conclusions: We conclude that in AD skin, the functional role played by S. aureus may depend on differential gene expression patterns and/or on post-translational modification mechanisms rather than being associated with peculiar genetic features.
    Keywords:  Staphylococcus aureus; antibiotic resistance; atopic dermatitis; biofilm; in silico genotype; pan-genome; whole-genome sequencing
  36. Microorganisms. 2023 May 25. pii: 1391. [Epub ahead of print]11(6):
      Candida albicans and Streptococcus mutans are known to synergistically interact with each other in the oral cavity. For example, glucosyltransferase B (GtfB), secreted by S. mutans, can bind to the C. albicans cell surface, promoting dual-species biofilm formation. However, the fungal factors mediating interactions with S. mutans are unknown. The C. albicans adhesins Als1, Als3, and Hwp1 are key players in C. albicans single-species biofilm formation, but their roles, if any, in interacting with S. mutans have not been assessed. Here, we investigated the roles of the C. albicans cell wall adhesins Als1, Als3, and Hwp1 on forming dual-species biofilms with S. mutans. We assessed the abilities of the C. albicans wild-type als1Δ/Δ, als3Δ/Δ, als1Δ/Δ/als3Δ/Δ, and hwp1Δ/Δ strains to form dual-species biofilms with S. mutans by measuring optical density, metabolic activity, cell enumeration, biomass, thickness, and architecture of the biofilms. We observed that the C. albicans wild-type strain formed enhanced dual-species biofilms in the presence of S. mutans in these different biofilm assays, confirming that C. albicans and S. mutans synergistically interact in the context of biofilms. Our results reveal that C. albicans Als1 and Hwp1 are major players in interacting with S. mutans, since dual-species biofilm formation was not enhanced when the als1Δ/Δ or hwp1Δ/Δ strains were cultured with S. mutans in dual-species biofilms. Als3, however, does not seem to play a clear role in interacting with S. mutans in dual-species biofilm formation. Overall, our data suggest that the C. albicans adhesins Als1 and Hwp1 function to modulate interactions with S. mutans and could be potential targets for future therapeutics.
    Keywords:  Als1; Candida albicans; Hwp1; Streptococcus mutans; biofilms; dual-species biofilms; interspecies interactions; microbiota; oral cavity; polymicrobial biofilms
  37. Pol Arch Intern Med. 2023 Jun 30. pii: 16520. [Epub ahead of print]
      Idiopathic pulmonary fibrosis (IPF) is a progressive and life-threatening interstitial lung disease of familial or sporadic onset. The incidence and prevalence of IPF is in the range of 0.09-1.30 and 0.33-4.51 per 10,000 persons, respectively. IPF has a poor prognosis, and death usually occurring within 2-5 years following the diagnosis due to secondary respiratory failure. Currently, there are two drugs available to treat IPF, prirfenidone and nintedanib, both only slow the disease progression and, in addition, have unfavorable safety profiles. IPF bears the histology of usual interstitial pneumonia, which is characterized by bronchiolization of distal airspaces, honeycombing, fibroblastic foci, and abnormal epithelial hyperplasia. In the last years, alterations in metabolic pathways, in particular, those associated with fatty acid (FA) metabolism have been link to the pathogenesis of lung fibrosis. Changes in FA profiles have been reported in lung tissue, plasma, and bronchoalveolar lavage fluid of IPF patients and have been found to correlate with the disease progression and outcome. In addition, they have been associated with the development of a pro-fibrotic phenotype of epithelial cells, macrophages, and fibroblasts/myofibroblasts contributing to their (trans)differentiation and production of disease relevant mediators. Furthermore, strategies focusing on the correction of FA profiles in experimental models of lung fibrosis brought advances in understanding tissue scarring processes and contributed to the transition of new molecules into clinical development. This review highlights the role of FA and their metabolites in IPF and provides evidence for therapeutic potential of lipidome manipulations in the treatment of this disease.
  38. Genome Biol Evol. 2023 Jun 30. pii: evad119. [Epub ahead of print]
      Detection of microbial pathogens is a primary function of many mammalian immune proteins. This is accomplished through the recognition of diverse microbial-produced macromolecules including proteins, nucleic acids and carbohydrates. Pathogens subvert host defenses by rapidly changing these structures to avoid detection, placing strong selective pressures on host immune proteins that repeatedly adapt to remain effective. Signatures of rapid evolution have been identified in numerous immunity proteins involved in the detection of pathogenic protein substrates, but whether similar signals can be observed in host proteins engaged in interactions with other types of pathogen-derived molecules has received less attention. This focus on protein-protein interfaces has largely obscured the study of fungi as contributors to host-pathogen conflicts, despite their importance as a formidable class of vertebrate pathogens. Here, we provide evidence that mammalian immune receptors involved in the detection of microbial glycans have been subject to recurrent positive selection. We find that rapidly evolving sites in these genes cluster in key functional domains involved in carbohydrate recognition. Further, we identify convergent patterns of substitution and evidence for balancing selection in one particular gene, MelLec, which plays a critical role in controlling invasive fungal disease. Our results also highlight the power of evolutionary analyses to reveal uncharacterized interfaces of host-pathogen conflict by identifying genes, like CLEC12A, with strong signals of positive selection across mammalian lineages. These results suggest that the realm of interfaces shaped by host-microbe conflicts extends beyond the world of host-viral protein-protein interactions and into the world of microbial glycans and fungi.
    Keywords:  balancing selection; evolutionary conflict; host-pathogen interactions; microbial glycans; pattern recognition receptor; rapid evolution