Microbiota-Dependent Regulation of Antimicrobial Immunity in the Lung

Comprehensive human respiratory genome catalogue underlies the high resolution and precision of the respiratory microbiome

The human respiratory microbiome plays a crucial role in respiratory health, but there is no comprehensive respiratory genome catalogue (RGC) for studying the microbiome. In this study, we collected whole-metagenome shotgun sequencing data from 4067 samples and sequenced long reads of 124 samples, yielding 9.08 and 0.42 Tbp of short- and long-read data, respectively. By submitting these data with a novel assembly algorithm, we obtained a comprehensive human RGC. This high-quality RGC contains 190,443 contigs over 1 kbps and an N50 length exceeding 13 kbps; it comprises 159 high-quality and 393 medium-quality genomes, including 117 previously uncharacterized respiratory bacteria. Moreover, the RGC contains 209 respiratory-specific species not captured by the unified human gastrointestinal genome. Using the RGC, we revisited a study on a pediatric pneumonia dataset and identified 17 pneumonia-specific respiratory pathogens, reversing an inaccurate etiological conclusion due to the previous incomplete reference. Furthermore, we applied the RGC to the data of 62 participants with a clinical diagnosis of infection. Compared to the Nucleotide database, the RGC yielded greater specificity (0 versus 0.444, respectively) and sensitivity (0.852 versus 0.881, respectively), suggesting that the RGC provides superior sensitivity and specificity for the clinical diagnosis of respiratory diseases.

Clinically used broad-spectrum antibiotics compromise inflammatory monocyte-dependent antibacterial defense in the lung

Hospital-acquired pneumonia (HAP) is associated with high mortality and costs, and frequently caused by multidrug-resistant (MDR) bacteria. Although prior antimicrobial therapy is a major risk factor for HAP, the underlying mechanism remains incompletely understood. Here, we demonstrate that antibiotic therapy in hospitalized patients is associated with decreased diversity of the gut microbiome and depletion of short-chain fatty acid (SCFA) producers. Infection experiments with mice transplanted with patient fecal material reveal that these antibiotic-induced microbiota perturbations impair pulmonary defense against MDR Klebsiella pneumoniae. This is dependent on inflammatory monocytes (IMs), whose fatty acid receptor (FFAR)2/3-controlled and phagolysosome-dependent antibacterial activity is compromized in mice transplanted with antibiotic-associated patient microbiota. Collectively, we characterize how clinically relevant antibiotics affect antimicrobial defense in the context of human microbiota, and reveal a critical impairment of IM´s antimicrobial activity. Our study provides additional arguments for the rational use of antibiotics and offers mechanistic insights for the development of novel prophylactic strategies to protect high-risk patients from HAP.

Liu Shen Capsule Alters Airway Microbiota Composition and Metabolite Profiles in Healthy Humans

Alteration in airway microbiota composition and perturbations in microbe-metabolites interactions have been proposed as markers of many diseases. Liu Shen (LS) capsule, a traditional Chinese medicine, was proved as favorable in treating respiratory diseases. However, the effects of the LS capsule in terms of regulating human microorganisms and metabolite profiles are not well known. This study aimed to define and compare the respiratory microbiota composition and circulating and fecal metabolite profiles before and after LS capsule administration. A total of 30 healthy volunteers were recruited. The pharyngeal swab samples were collected for 16S rRNA gene sequencing. The serum and fecal samples were collected to analyze the non-targeted ultra-performance liquid chromatography-tandem mass spectrometry metabolomics. The airway microbial compositions were profoundly altered after LS capsule administration, as evidenced by increased microbial diversity and altered microbial taxa distribution. The increasing abundance of bacterial Bifidobacteria, and Lactobacillus characterized the after-administration groups, and the increasing of abundance bacterial Proteobacteria, Veillonella, Prevotella, Neisseria, and Actinomyces characterized the before-administration groups. Significant discriminations were observed in both serum and fecal metabolic profiles between the before- and after-administration groups. A total number of 134 and 71 significant HMDB taxonomic metabolites including glycerophospholipids, fatty acyls, and prenol lipids in the serum and fecal samples were identified respectively between the before- and after-administration groups. The integrated analysis showed that some altered airway microbiota phylum, such as Bacteroidetes and Proteobacteria, significantly correlated with metabolites in serum and fecal. Hence, our study reported the alternations in the composition and functions of the airway microbial community and the changes in circulating and fecal metabolite profiles after LS capsule administration in healthy humans, thus providing a novel insight into the mechanisms underlying the role of LS capsule treating and preventing related diseases.

Leptin in the Respiratory Tract: Is There a Role in SARS-CoV-2 Infection?

Leptin is a pleiotropic adipocytokine involved in several physiologic functions, with a known role in innate and adaptive immunity as well as in tissue homeostasis. Long- and short-isoforms of leptin receptors are widely expressed in many peripheral tissues and organs, such as the respiratory tract. Similar to leptin, microbiota affects the immune system and may interfere with lung health through the bidirectional crosstalk called the “gut-lung axis.” Obesity leads to impaired protective immunity and altered susceptibility to pulmonary infections, as those by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although it is known that leptin and microbiota link metabolism and lung health, their role within the SARS-CoV2 coronavirus disease 2019 (COVID-19) deserves further investigations. This review aimed to summarize the available evidence about: (i) the role of leptin in immune modulation; (ii) the role of gut microbiota within the gut-lung axis in modulating leptin sensitivity; and (iii) the role of leptin in the pathophysiology of COVID-19.

Maternal gut microbiome regulates immunity to RSV infection in offspring

Development of the immune system can be influenced by diverse extrinsic and intrinsic factors that influence the risk of disease. Severe early life respiratory syncytial virus (RSV) infection is associated with persistent immune alterations. Previously, our group had shown that adult mice orally supplemented with Lactobacillus johnsonii exhibited decreased airway immunopathology following RSV infection. Here, we demonstrate that offspring of mice supplemented with L. johnsonii exhibit reduced airway mucus and Th2 cell–mediated response to RSV infection. Maternal supplementation resulted in a consistent gut microbiome in mothers and their offspring. Importantly, supplemented maternal plasma and breastmilk, and offspring plasma, exhibited decreased inflammatory metabolites. Cross-fostering studies showed that prenatal Lactobacillus exposure led to decreased Th2 cytokines and lung inflammation following RSV infection, while postnatal Lactobacillus exposure diminished goblet cell hypertrophy and mucus production in the lung in response to airway infection. These studies demonstrate that Lactobacillus modulation of the maternal microbiome and associated metabolic reprogramming enhance airway protection against RSV in neonates.

Association between Gut Microbiota and Development of Gestational Diabetes Mellitus

Background: It is well known that women with gestational diabetes mellitus (GDM) have gut dysbiosis. However, the dynamic alterations of gut microbiota in GDM are unclear. Additionally, the effects of maternal gut microbiota on the gut microbiota of their newborns remains controversial. The primary objective of this study is to determine the association between types and amounts of gut microbiota and development of gestational diabetes mellitus (GDM). Methods: Eighty-eight pregnant women, including 39 non-GDM and 49 GDM, and their 88 offspring were enrolled. Maternal feces were collected at the time of GDM diagnosis (24–28 weeks of gestation) and at before delivery (≥37 weeks of gestation). Meconium and the first feces of their newborns were also obtained. Results: from quantitative polymerase chain reaction (qPCR) showed that maternal Lactobacillales was decreased from baseline to the time before delivery in both non-GDM and GDM. Firmicutes/Bacteroidetes (F/B) ratio at before delivery was higher in the GDM group. However, there was no difference of neonatal gut microbiota between groups. Conclusions: Although we found only few gut microbiota that demonstrated the difference between GDM and non-GDM, gut microbiota may play a more important role in the development of severer GDM. Therefore, a further study comparing the gut microbiota composition among non-GDM, GDM with diet modification only, GDM with insulin therapy, GDM with successful treatment, and GDM with failure of treatment is needed.

Different aspects of frailty and COVID-19: points to consider in the current pandemic and future ones

BACKGROUND

Older adults at a higher risk of adverse outcomes and mortality if they get infected with Severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2). These undesired outcomes are because ageing is associated with other conditions like multimorbidity, frailty and disability. This paper describes the impact of frailty on coronavirus disease 2019 (COVID-19) management and outcomes. We also try to point out the role of inflamm-ageing, immunosenescence and reduced microbiota diversity in developing a severe form of COVID-19 and a different response to COVID-19 vaccination among older frail adults. Additionally, we attempt to highlight the impact of frailty on intensive care unit (ICU) outcomes, and hence, the rationale behind using frailty as an exclusion criterion for critical care admission. Similarly, the importance of using a time-saving, validated, sensitive, and user-friendly tool for frailty screening in an acute setting as COVID-19 triage. We performed a narrative review. Publications from 1990 to March 2021 were identified by searching the electronic databases MEDLINE, CINAHL and SCOPUS. Based on this search, we have found that in older frail adults, many mechanisms contribute to the severity of COVID-19, particularly cytokine storm; those mechanisms include lower immunological capacity and status of ongoing chronic inflammation and reduced gut microbiota diversity. Higher degrees of frailty were associated with poor outcomes and higher mortality rates during and after ICU admission. Also, the response to COVID-19 vaccination among frail older adults might differ from the general population regarding effectiveness and side effects. Researches also had shown that there are many tools for identifying frailty in an acute setting that could be used in COVID-19 triage, and before ICU admission, the clinical frailty scale (CFS) was the most recommended tool.

CONCLUSION

Older frail adults have a pre-existing immunopathological base that puts them at a higher risk of undesired outcomes and mortality due to COVID-19 and poor response to COVID-19 vaccination. Also, their admission in ICU should depend on their degree of frailty rather than their chronological age, which is better to be screened using the CFS.

Lung microbiota predict invasive pulmonary aspergillosis and its outcome in immunocompromised patients

Rationale

Recent studies have revealed that the lung microbiota of critically ill patients is altered and predicts clinical outcomes. The incidence of invasive fungal infections, namely, invasive pulmonary aspergillosis (IPA), in immunocompromised patients is increasing, but the clinical significance of variations in lung bacterial communities is unknown.

Objectives

To define the contribution of the lung microbiota to the development and course of IPA.

Methods and measurements

We performed an observational cohort study to characterise the lung microbiota in 104 immunocompromised patients using bacterial 16S ribosomal RNA gene sequencing on bronchoalveolar lavage samples sampled on clinical suspicion of infection. Associations between lung dysbiosis in IPA and pulmonary immunity were evaluated by quantifying alveolar cytokines and chemokines and immune cells. The contribution of microbial signatures to patient outcome was assessed by estimating overall survival.

Main results

Patients diagnosed with IPA displayed a decreased alpha diversity, driven by a markedly increased abundance of the Staphylococcus, Escherichia, Paraclostridium and Finegoldia genera and a decreased proportion of the Prevotella and Veillonella genera. The overall composition of the lung microbiome was influenced by the neutrophil counts and associated with differential levels of alveolar cytokines. Importantly, the degree of bacterial diversity at the onset of IPA predicted the survival of infected patients.

Conclusions

Our results reveal the lung microbiota as an understudied source of clinical variation in patients at risk of IPA and highlight its potential as a diagnostic and therapeutic target in the context of respiratory fungal diseases.

Toll-like receptors, environmental caging, and lung dysbiosis

Recent studies have implicated lung microbiota in shaping local alveolar immune responses. Toll-like receptors are major sensors of microbiota and determinants of local epithelial homeostasis. The impact of toll-like receptor deficiency on lung microbiota is unknown. To determine whether the absence of toll-like receptors results in altered lung microbiota or dysbiosis, we compared lung microbiota in wild-type and toll-like receptor-deficient experimental mice using 16S ribosomal RNA gene quantification and sequencing. We used a randomized environmental caging strategy to determine the impact of toll-like receptors on lung microbiota. Lung microbiota are detectable in toll-like receptor-deficient experimental mice and exhibit considerable variability. The lung microbiota of toll-like receptor-deficient mice are altered in community composition (PERMANOVA P < 0.001), display reduced diversity (t test P = 0.0075), and bacterial burden (t test P = 0.016) compared with wild-type mice with intact toll-like receptors and associated signaling pathways. The lung microbiota of wild-type mice when randomized to cages with toll-like receptor-deficient mice converged with no significant difference in community composition (PERMANOVA P > 0.05) after 3 wk of cohousing. The lung microbiome of toll-like receptor-deficient mice is distinct from wild-type mice and may be less susceptible to the effects of caging as an environmental variable. Our observations support a role for toll-like receptor signaling in the shaping of lung microbiota.

Search for Promising Strains of Probiotic Microbiota Isolated from Different Biotopes of Healthy Cats for Use in the Control of Surgical Infections

Despite the introduction of modern methods of treatment, the creation of new generations of antibacterial agents, and the constant improvement of aseptic and antiseptic methods, the treatment of purulent–inflammatory processes remains one of the most complex and urgent problems in veterinary practice. The article presents the results of the isolation of indigenous microbiota from various biotopes of healthy cats, as well as the study of their biological marker properties for the selection of the most optimal strains in probiotic medicines for the control of surgical infections. It was demonstrated that isolated cultures of bifidobacteria and lactobacilli, which we isolated, revealed high sensitivity to antibiotics of the β-lactam group (excepting L. acidophilus No. 24, L. plantarum “Victoria” No. 22, L. rhamnosus No. 5, L. rhamnosus No. 20, and L. rhamnosus No. 26, which showed a significant variability in sensitivity to antibacterial drugs of this group, indicating the great potential of these microorganisms) and resistance to aminoglycosides, lincosamides, and fluoroquinolones (with the exception of gatifloxacin, which showed high efficiency in relation to all lactic acid microorganisms). The adhesive properties of the isolated lactobacteria and bifidobacteria were variable, even within the same species. It was found that the B. adolescentis No. 23 strain of the Bifidobacterium genus, as well as the L. plantarum No. 8, L. plantarum “Victoria” No. 22, L. rhamnosus No. 6, L. rhamnosus No. 26, L. acidophilus No. 12, and L. acidophilus No. 24 strains of the Lactobacillus genus had the highest adhesive activity. Thus, when conducting a detailed analysis of the biological marker properties of candidate cultures (determining their sensitivity to antimicrobial agents, studying the adhesive properties, and antagonistic activity in relation to causative agents of surgical infection in cats), it was found that the most promising are L. plantarum “Victoria” No. 22, L. rhamnosus No. 26, and L. acidophilus No. 24.

The impact of the Fungus-Host-Microbiota interplay upon Candida albicans infections: current knowledge and new perspectives

Candida albicans is a major fungal pathogen of humans. It exists as a commensal in the oral cavity, gut or genital tract of most individuals, constrained by the local microbiota, epithelial barriers and immune defences. Their perturbation can lead to fungal outgrowth and the development of mucosal infections such as oropharyngeal or vulvovaginal candidiasis, and patients with compromised immunity are susceptible to life-threatening systemic infections. The importance of the interplay between fungus, host and microbiota in driving the transition from C. albicans commensalism to pathogenicity is widely appreciated. However, the complexity of these interactions, and the significant impact of fungal, host and microbiota variability upon disease severity and outcome, are less well understood. Therefore, we summarise the features of the fungus that promote infection, and how genetic variation between clinical isolates influences pathogenicity. We discuss antifungal immunity, how this differs between mucosae, and how individual variation influences a person's susceptibility to infection. Also, we describe factors that influence the composition of gut, oral and vaginal microbiotas, and how these affect fungal colonisation and antifungal immunity. We argue that a detailed understanding of these variables, which underlie fungal-host-microbiota interactions, will present opportunities for directed antifungal therapies that benefit vulnerable patients.

Impacts of gut microbiota on gestational diabetes mellitus: a comprehensive review

BACKGROUND

Gestational diabetes mellitus (GDM) is a condition that seriously threatens mother and child health. The incidence of GDM has increased worldwide in the past decades. In addition, the complications of GDM such as type 2 diabetes (T2DM) and neonatal malformations could negatively affect the living quality of mothers and their children.

AIM

It has been widely known that the imbalance of gut microbiota or called 'gut dysbiosis' plays a key role in the development of insulin resistance and chronic low-grade inflammation in T2DM patients. However, the impacts of gut microbiota on GDM remain controversial. Here, we aim to comprehensively review the alterations of gut microbiota in GDM mothers and their offspring.

RESULTS

The alterations of Firmicutes/Bacteroidetes (F/B) ratio, short-chain fatty acid (SCFA)-producing bacteria, bacteria with probiotics properties and gram-negative lipopolysaccharide (LPS)-producing bacteria play a vital role in the development of GDM. The beneficial roles of gut microbiota modification (probiotics, synbiotics and lifestyle modification) as a treatment of GDM were found in some, but not all studies.

CONCLUSION

In the near future, gut microbiota modification may be considered as one of the standard treatments for GDM. Moreover, further studies regarding the specific gut microbiota that are associated with the early development of GDM are required. This may contribute to the novel diagnostic markers for early stages of GDM.

The microbiota in pneumonia: From protection to predisposition

Mucosal surfaces of the upper respiratory tract and gut are physiologically colonized with their own collection of microbes, the microbiota. The normal upper respiratory tract and gut microbiota protects against pneumonia by impeding colonization by potentially pathogenic bacteria and by regulating immune responses. However, antimicrobial therapy and critical care procedures perturb the microbiota, thus compromising its function and predisposing to lung infections (pneumonia). Interindividual variations and age-related alterations in the microbiota also affect vulnerability to pneumonia. We discuss how the healthy microbiota protects against pneumonia and how host factors and medical interventions alter the microbiota, thus influencing susceptibility to pneumonia.