Active and Secretory IgA-Coated Bacterial Fractions Elucidate Dysbiosis in Clostridium difficile Infection

Applied physiology: gut microbiota and antimicrobial therapy

The gut microbiota plays an important role in maintaining human health and in the pathogenesis of several diseases. Antibiotics are among the most commonly prescribed drugs and have a significant impact on the structure and function of the gut microbiota. The understanding that a healthy gut microbiota prevents the development of many diseases has also led to its consideration as a potential therapeutic target. At the same time, any factor that alters the gut microbiota becomes important in this approach. Exercise and antibacterial therapy have a direct effect on the microbiota. The review reflects the current state of publications on the mechanisms of intestinal bacterial involvement in the pathogenesis of cardiovascular, metabolic, and neurodegenerative diseases. The physiological mechanisms of the influence of physical activity on the composition of the gut microbiota are considered. The mechanisms of the common interface between exercise and antibacterial therapy will be considered using the example of several socially important diseases. The aim of the study is to show the physiological relationship between the effects of exercise and antibiotics on the gut microbiota.

Engineered Secretory Immunoglobulin A provides insights on antibody-based effector mechanisms targeting Clostridiodes difficile

Secretory (S) Immunoglobin (Ig) A is the predominant mucosal antibody, which mediates host interactions with commensal and pathogenic microbes, including Clostridioides difficile. SIgA adopts a polymeric IgA structure that is bound by secretory component (SC). Despite significance, how SIgA supports diverse effector mechanisms is poorly characterized and SIgA-based therapies nonexistent. We engineered chimeric (c) SIgAs, in which we replaced SC domain D2 with a single domain antibody or a monomeric fluorescent protein, allowing us to investigate and enhance SIgA effector mechanisms. cSIgAs exhibited increased neutralization potency against C. difficile toxins, promoted bacterial clumping and cell rupture, and decreased cytotoxicity. cSIgA also allowed us to visualize and/or quantify C. difficile morphological changes and clumping events. Results reveal mechanisms by which SIgA combats C. difficile infection, demonstrate that cSIgA design can modulate these mechanisms, and demonstrate cSIgA's adaptability to modifications that might target a broad range of antigens and effector mechanisms.

Intestinal IgA-Coated Bacteria in Healthy- and Altered-Microbiomes (Dysbiosis) and Predictive Value in Successful Fecal Microbiota Transplantation

IgA-coated bacteria in the gut (IgA-biome) provide a homeostatic function in healthy people through inhibition of microbial invaders and by protecting the epithelial monolayer of the gut. The laboratory methods used to detect this group of bacteria require flow cytometry and DNA sequencing (IgA-Seq). With dysbiosis (reduced diversity of the microbiome), the IgA-biome also is impaired. In the presence of enteric infection, oral vaccines, or an intestinal inflammatory disorder, the IgA-biome focuses on the pathogenic bacteria or foreign antigens, while in other chronic diseases associated with dysbiosis, the IgA-biome is reduced in capacity. Fecal microbiota transplantation (FMT), the use of fecal product from well-screened, healthy donors administered to patients with dysbiosis, has been successful in engrafting the intestine with healthy microbiota and metabolites leading to improve health. Through FMT, IgA-coated bacteria have been transferred to recipients retaining their immune coating. The IgA-biome should be evaluated in FMT studies as these mucosal-associated bacteria are more likely to be associated with successful transplantation than free luminal organisms. Studies of the microbiome pre- and post-FMT should employ metagenomic methods that identify bacteria at least at the species level to better identify organisms of interest while allowing comparisons of microbiota data between studies.

Robust Classification Using Posterior Probability Threshold Computation Followed by Voronoi Cell Based Class Assignment Circumventing Pitfalls of Bayesian Analysis of Biomedical Data

Bayesian inference is ubiquitous in science and widely used in biomedical research such as cell sorting or “omics” approaches, as well as in machine learning (ML), artificial neural networks, and “big data” applications. However, the calculation is not robust in regions of low evidence. In cases where one group has a lower mean but a higher variance than another group, new cases with larger values are implausibly assigned to the group with typically smaller values. An approach for a robust extension of Bayesian inference is proposed that proceeds in two main steps starting from the Bayesian posterior probabilities. First, cases with low evidence are labeled as “uncertain” class membership. The boundary for low probabilities of class assignment (threshold ε) is calculated using a computed ABC analysis as a data-based technique for item categorization. This leaves a number of cases with uncertain classification (p < ε). Second, cases with uncertain class membership are relabeled based on the distance to neighboring classified cases based on Voronoi cells. The approach is demonstrated on biomedical data typically analyzed with Bayesian statistics, such as flow cytometric data sets or biomarkers used in medical diagnostics, where it increased the class assignment accuracy by 1−10% depending on the data set. The proposed extension of the Bayesian inference of class membership can be used to obtain robust and plausible class assignments even for data at the extremes of the distribution and/or for which evidence is weak.

Shared and Non-Shared sIgA-Coated and -Uncoated Bacteria in Intestine of Mother–Infant Pairs

The infant gut microbiota is critical for promoting and maintaining early-life health. The study aimed to analyze the composition of sIgA-coated and sIgA-uncoated bacterial communities at genus level and lactobacilli and bifidobacterial communities at species level in human breast milk (HBM) and infant and maternal feces. Eleven pregnant women were recruited successfully. HBM; infant feces during colostrum, transition, and mature stages; and maternal feces within the mature stage were collected. sIgA-coated and sIgA-uncoated bacteria were separated with magnetic-activated cell sorting. Then, 16S rRNA sequencing, bifidobacterial groEL gene sequencing, and lactobacilli groEL gene sequencing were performed to analyze the bacterial community. PCoA revealed that the compositions of sIgA-coated and sIgA-uncoated bacteria were different among HBM and infant and maternal feces. Higher relative abundance of sIgA-uncoated Bifidobacterium was found in the three lactation stages in infant feces compared to the corresponding HBM, and a higher relative abundance of sIgA-uncoated Faecalibacterium was found in maternal feces compared to HBM and infant feces. For bifidobacterial community, sIgA-coated and sIgA-uncoated B. longum subsp. infantis and B. pseudocatenulatum was dominant in infant feces and maternal feces, respectively. The relative abundance of sIgA-uncoated B. longum subsp. infantis was significantly higher in infant feces compared to that in maternal feces. For the Lactobacillus community, L. paragasseri and L. mucosae were dominant in infant and maternal feces, respectively. HBM and infant and maternal feces showed distinct diversity and composition of both sIgA-coated and sIgA-uncoated bacteria at genus level. Infant and maternal feces showed similar composition of Bifidobacterium at species level. The same Bifidobacterium species could be detected both in sIgA-coated and -uncoated form. This article provided deeper understanding on the microbiota profile in HBM and infant and maternal feces.

Roles of Secretory Immunoglobulin A in Host-Microbiota Interactions in the Gut Ecosystem

In the gastrointestinal tract (GIT), the immune system interacts with a variety of microorganisms, including pathogens as well as beneficial symbionts that perform important physiological functions for the host and are crucial to sustain intestinal homeostasis. In normal conditions, secretory immunoglobulin A (SIgA) is the principal antibody produced by B cells in the GIT mucosa. Polyreactivity provides certain SIgA molecules with the ability of binding different antigens in the bacterial surface, such as O-antigens and teichoic acids, while cross-species reactivity allows them to recognize and interact with different types of bacteria. These functions may be crucial in allowing SIgA to modulate the complex gut microbiota in an efficient manner. Several studies suggest that SIgA can help with the retention and proliferation of helpful members of the gut microbiota. Gut microbiota alterations in people with IgA deficiency include the lack of some species that are known to be normally coated by SIgA. Here, we discuss the different ways in which SIgA behaves in relation to pathogens and beneficial bacteria of the gut microbiota and how the immune system might protect and facilitate the establishment and maintenance of certain gut symbionts.

The Probiotic Strain Bifidobacterium animalis ssp. lactis HY8002 Potentially Improves the Mucosal Integrity of an Altered Intestinal Microbial Environment

Intestinal microbiota mediate the development and regulation of the intestinal immune system either directly or indirectly. Particularly, Bifidobacterium spp. play an important role in regulating the intestinal immunity and intestinal barrier. We demonstrated that Bifidobacterium animalis ssp. lactis HY8002, selected from eight Bifidobacterium strains by in vitro experimentation, had exceptional resistance to digestive tract conditions and high adhesion to intestinal epithelial cells and a positive effect on immunoglobulin A (IgA) secretion by Peyer’s patch cells. Moreover, HY8002 restored the expression of tight junction-related genes, initially reduced by lipopolysaccharide treatment, to normal levels in human intestinal epithelial cells. Notably, HY8002 restored kanamycin-induced reduction in Peyer’s patch cell numbers, serum and fecal IgA levels, and zonula occludens 1 and Toll-like receptor 2 levels in the mouse small intestine. In addition, HY8002 restores microbiome composition disturbed by kanamycin, and these microbiome changes have been found to correlate with TLR2 levels in the small intestine. Moreover, the ability of HY8002 to enhance IgA in Peyer’s patch cells and ZO-1 levels in intestinal epithelial cells was significantly inhibited by a TLR2 blocking antibody, which suggests that the HY8002 improve intestinal barrier function via TLR2. Finally, whole-genome sequencing of HY8002 revealed that it did not possess any known virulence factors. Therefore, HY8002 is a promising, functional probiotic supplement to improve intestinal barrier function by improving intestinal immunity and microbiota balance.

Impact of dietary fructooligosaccharides (FOS) on murine gut microbiota and intestinal IgA secretion

Fructooligosaccharides (FOS) are considered as prebiotics and are well known for their health-promoting properties, including antitumor, allergy-preventive, and infection-protective effects. They exert these effects by modulating the gut microbial composition and dynamics. In the present study, we performed a comparative whole metagenome shotgun sequencing analysis (WMGS) to elucidate the gut microbiota and secretary Immunoglobulin A (SIgA) dynamics as a result of 5% (w/w) FOS supplementation over a period of 7 days (fecal samples were collected every day). A number of taxa including Bacteroides, Lactobacillus, Roseburia, Clostridia, Faecalibaculum, and Enterorhabdus were found to be modulated with SIgA production in the murine gut. The process of SIgA production from FOS metabolization was found to be carried out via the production of short-chain fatty acids in the gut. Species of Bacteroides and Roseburia; namely, B. caccae, B. finegoldii, B. ovatus, B. thetaiotamicron, and Roseburia intestinalis, respectively, are predominantly responsible for FOS metabolization in the murine gut. The abundances of these bacterial species and their corresponding functions involved in FOS metabolization decreased over time even though these prebiotics were administered continuously for seven days. This suggests that there is a decrease in FOS metabolization over time. In addition, the present analysis suggests that the administration of FOS may help to reduce the pathogenic bacteria from the gut via SIgA production.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-022-03116-3.

Crosstalk between sIgA-Coated Bacteria in Infant Gut and Early-Life Health

Gut microbiota transmission from mother to offspring has attracted much interest in recent years. The gut microbiota in the infant plays a potentially significant role in modulating and maintaining the development of infant immunity. Secretory immunoglobulin A (sIgA), the major immunoglobulin in the intestine, can target polysaccharides and flagellin on the bacterial surface, resulting in sIgA-coated bacteria. The presentation of specific bacteria coated with sIgA may be a signal of disease and provide novel insights into the relationship between infant microbiota and disease. Here, we review the composition of sIgA-coated bacteria in the adult intestine, human milk, and the infant intestine, as well as the factors that influence the development of gut microbiota in early life. Then, we highlight the diseases that are related to variations in sIgA-coated bacteria in the infant and adult intestine. Furthermore, we discuss the possibility that sIgA-coated bacteria could play a role in mediating both innate and adaptive immune responses. Finally, we propose directions for future research to promote our understanding within this field.

Characterization of intestinal microbiota and fecal cortisol, T3, and IgA in forest musk deer (Moschus berezovskii) from birth to weaning

Analysis of the intestinal microbiota and physiological parameters in mammalian infancy can reveal health status. In this study, we used a combination of molecular and immunochemical approaches to assess fecal microbiota as well as Cortisol (Cor), Triiodothyronine (T3), and immunoglobulin A (IgA) levels of young forest musk deer (FMD), from birth to one month after weaning (7 days of age-110 days of age). During development as the diet of FMD changes from consuming milk to eating plants, the richness and diversity of intestinal microbiota of young FMD increased significantly. Cor levels remained unchanged throughout early development while significantly increased after weaning, T3 and IgA initially were derived from milk during lactation, significantly decreased after weaning. Correlation network analysis showed that the community of food-oriented microbes were highly structured and that many genera were correlated. Overall, this study provides scientific insights into effective management strategies for the protection of FMD population.

Detection of mixed-strain infections by FACS and ultra-low input genome sequencing

The epidemiological tracking of a bacterial outbreak may be jeopardized by the presence of multiple pathogenic strains in one patient. Nevertheless, this fact is not considered in most of the epidemiological studies and only one colony per patient is sequenced. On the other hand, the routine whole genome sequencing of many isolates from each patient would be costly and unnecessary, because the number of strains in a patient is never known a priori. In addition, the result would be biased by microbial culture conditions. Herein we propose an approach for detecting mixed-strain infection, providing C. difficile infection as an example. The cells of the target pathogenic species are collected from the bacterial suspension by the fluorescence activated cell sorting (FACS) and a shallow genome sequencing is performed. A modified sequencing library preparation protocol for low-input DNA samples can be used for low prevalence gut pathogens (< 0.1% of the total microbiome). This FACS-seq approach reduces diagnostics time (no culture is needed) and may promote discoveries of novel strains. Methodological details, possible issues and future directions for the sequencing of these natural pan-genomes are herein discussed.

The antibody/microbiota interface in health and disease

The human intestine is densely colonized with commensal microbes that stimulate the immune system. While secretory Immunoglobulin (Ig) A is known to play a crucial role in gut microbiota compartmentalization, secretory IgM, and systemic IgG have recently been highlighted in host-microbiota interactions as well. In this review, we discuss important aspects of secretory IgA biology, but rather than focusing on mechanistic aspects of IgA impact on microbiota, we stress the current knowledge of systemic antibody responses to whole gut microbiota, in particular their generation, specificities, and function. We also provide a comprehensive picture of secretory IgM biology. Finally, therapeutic and diagnostic implications of these novel findings for the treatment of various diseases are outlined.

Gut Microbiota Modulation on Intestinal Mucosal Adaptive Immunity

The mammalian intestine harbors a remarkable number of microbes and their components and metabolites, which are fundamental for the instigation and development of the host immune system. The intestinal innate and adaptive immunity coordinate and interact with the symbionts contributing to the intestinal homeostasis through establishment of a mutually beneficial relationship by tolerating to symbiotic microbiota and retaining the ability to exert proinflammatory response towards invasive pathogens. Imbalance between the intestinal immune system and commensal organisms disrupts the intestinal microbiological homeostasis, leading to microbiota dysbiosis, compromised integrity of the intestinal barrier, and proinflammatory immune responses towards symbionts. This, in turn, exacerbates the degree of the imbalance. Intestinal adaptive immunity plays a critical role in maintaining immune tolerance towards symbionts and the integrity of intestinal barrier, while the innate immune system regulates the adaptive immune responses to intestinal commensal bacteria. In this review, we will summarize recent findings on the effects and mechanisms of gut microbiota on intestinal adaptive immunity and the plasticity of several immune cells under diverse microenvironmental settings.

Oral Administration of Compound Probiotics Improved Canine Feed Intake, Weight Gain, Immunity and Intestinal Microbiota

Probiotics have been used successfully to promote human and animal health, but only limited studies have focused on using probiotics to improve the health of hosts of different age. Canine microbiome studies may be predictive of results in humans because of the high structural and functional similarity between dog and human microbiomes. A total of 90 dogs were divided into three groups based on dog age (elderly group, n = 30; young group, n = 24; and training group, n = 36). Each group was subdivided into two subgroups, with and without receiving daily probiotic feed additive. The probiotic feed additive contained three different bacterial strains, namely Lactobacillus casei Zhang, Lactobacillus plantarum P-8, and Bifdobacterium animalis subsp. lactis V9. Serum and fecal samples were collected and analyzed at four different time points, i.e., days 0, 30, and 60 of probiotic treatment, and 15 days after ceasing probiotic treatment. The results demonstrated that probiotics significantly promoted the average daily feed intake of the elderly dogs (P < 0.01) and the average daily weight gain of all dogs (P < 0.05), enhanced the level of serum IgG (P < 0.001), IFN-α (P < 0.05), and fecal SIgA (P < 0.001), while reduced the TNF-α (P < 0.05). Additionally, probiotics could change the gut microbial structure of elderly dogs and significantly increased beneficial bacteria (including some Lactobacillus species and Faecalibacterium prausnitzii) and decreased potentially harmful bacteria (including Escherichia coli and Sutterella stercoricanisin), and the elderly dogs showed the strongest response to the probiotics; the relative abundance of some of these species correlated with certain immune factors and physiological parameters, suggesting that the probiotic treatment improved the host health and enhanced the host immunity by stimulating antibody and cytokine secretion through regulating canine gut microbiota. Furthermore, the gut microbiota of the elderly dogs shifted toward a younger-like composition at day 60 of probiotic treatment. Our findings suggested that the probiotic treatment effects on canine health and immunity were age-related and have provided interesting insights into future development of probiotic-based strategies to improve animal and human health.

Carotenoid supplementation and retinoic acid in immunoglobulin A regulation of the gut microbiota dysbiosis

Dysbiosis, a broad spectrum of imbalance of the gut microbiota, may progress to microbiota dysfunction. Dysbiosis is linked to some human diseases, such as inflammation-related disorders and metabolic syndromes. However, the underlying mechanisms of the pathogenesis of dysbiosis remain elusive. Recent findings suggest that the microbiome and gut immune responses, like immunoglobulin A production, play critical roles in the gut homeostasis and function, and the progression of dysbiosis. In the past two decades, much progress has been made in better understanding of production of immunoglobulin A and its association with commensal microbiota. The present minireview summarizes the recent findings in the gut microbiota dysbiosis and dysfunction of immunoglobulin A induced by the imbalance of pathogenic bacteria and commensal microbiota. We also propose the potentials of dietary carotenoids, such as β-carotene and astaxanthin, in the improvement of the gut immune system maturation and immunoglobulin A production, and the consequent promotion of the gut health. Impact statement The concept of carotenoid metabolism in the gut health has not been well established in the literature. Here, we review and discuss the roles of retinoic acid and carotenoids, including pro-vitamin A carotenoids and xanthophylls in the maturation of the gut immune system and IgA production. This is the first review article about the carotenoid supplements and the metabolites in the regulation of the gut microbiome. We hope this review would provide a new direction for the management of the gut microbiota dysbiosis by application of bioactive carotenoids and the metabolites.

Complementary Methodologies To Investigate Human Gut Microbiota in Host Health, Working towards Integrative Systems Biology

In 1680, Antonie van Leeuwenhoek noted compositional differences in his oral and fecal microbiota, pioneering the study of the diversity of the human microbiome. From Leeuwenhoek's time to successful modern attempts at changing the gut microbial landscape to cure disease, there has been an exponential increase in the recognition of our resident microbes as part of ourselves. Thus, the human host and microbiome have evolved in parallel to configure a balanced system in which microbes survive in homeostasis with our innate and acquired immune systems, unless disease occurs. A growing number of studies have demonstrated a correlation between the presence/absence of microbial taxa and some of their functional molecules (i.e., genes, proteins, and metabolites) with health and disease states. Nevertheless, misleading experimental design on human subjects and the cost and lack of standardized animal models pose challenges to answering the question of whether changes in microbiome composition are cause or consequence of a certain biological state. In this review, we evaluate the state of the art of methodologies that enable the study of the gut microbiome, encouraging a change in broadly used analytic strategies by choosing effector molecules (proteins and metabolites) in combination with coding nucleic acids. We further explore microbial and effector microbial product imbalances that relate to disease and health.

Oxidative stress in the oral cavity is driven by individual-specific bacterial communities

The term "bacterial dysbiosis" is being used quite extensively in metagenomic studies, however, the identification of harmful bacteria often fails due to large overlap between the bacterial species found in healthy volunteers and patients. We hypothesized that the pathogenic oral bacteria are individual-specific and they correlate with oxidative stress markers in saliva which reflect the inflammatory processes in the oral cavity. Temporally direct and lagged correlations between the markers and bacterial taxa were computed individually for 26 volunteers who provided saliva samples during one month (21.2 ± 2.7 samples/volunteer, 551 samples in total). The volunteers' microbiomes differed significantly by their composition and also by their degree of microbiome temporal variability and oxidative stress markers fluctuation. The results showed that each of the marker-taxa pairs can have negative correlations in some volunteers while positive in others. Streptococcus mutans, which used to be associated with caries before the metagenomics era, had the most prominent correlations with the oxidative stress markers, however, these correlations were not confirmed in all volunteers. The importance of longitudinal samples collections in correlation studies was underlined by simulation of single sample collections in 1000 different combinations which produced contradictory results. In conclusion, the distinct intra-individual correlation patterns suggest that different bacterial consortia might be involved in the oxidative stress induction in each human subject. In the future, decreasing cost of DNA sequencing will allow to analyze multiple samples from each patient, which might help to explore potential diagnostic applications and understand pathogenesis of microbiome-associated oral diseases.

Exploring the human microbiome from multiple perspectives: factors altering its composition and function

Our microbiota presents peculiarities and characteristics that may be altered by multiple factors. The degree and consequences of these alterations depend on the nature, strength and duration of the perturbations as well as the structure and stability of each microbiota. The aim of this review is to sketch a very broad picture of the factors commonly influencing different body sites, and which have been associated with alterations in the human microbiota in terms of composition and function. To do so, first, a graphical representation of bacterial, fungal and archaeal genera reveals possible associations among genera affected by different factors. Then, the revision of sequence-based predictions provides associations with functions that become part of the active metabolism. Finally, examination of microbial metabolite contents and fluxes reveals whether metabolic alterations are a reflection of the differences observed at the level of population structure, and in the last step, link microorganisms to functions under perturbations that differ in nature and aetiology. The utilisation of complementary technologies and methods, with a special focus on metabolomics research, is thoroughly discussed to obtain a global picture of microbiota composition and microbiome function and to convey the urgent need for the standardisation of protocols.

Antibiotic use and microbiome function

Our microbiome should be understood as one of the most complex components of the human body. The use of β-lactam antibiotics is one of the microbiome covariates that influence its composition. The extent to which our microbiota changes after an antibiotic intervention depends not only on the chemical nature of the antibiotic or cocktail of antibiotics used to treat specific infections, but also on the type of administration, duration and dose, as well as the level of resistance that each microbiota develops. We have begun to appreciate that not all bacteria within our microbiota are vulnerable or reactive to different antibiotic interventions, and that their influence on both microbial composition and metabolism may differ. Antibiotics are being used worldwide on a huge scale and the prescription of antibiotics is continuing to rise; however, their effects on our microbiota have been reported for only a limited number of them. This article presents a critical review of the antibiotics or antibiotic cocktails whose use in humans has been linked to changes in the composition of our microbial communities, with a particular focus on the gut, oral, respiratory, skin and vaginal microbiota, and on their molecular agents (genes, proteins and metabolites). We review the state of the art as of June 2016, and cover a total of circa 68 different antibiotics. The data herein are the first to compile information about the bacteria, fungi, archaea and viruses most influenced by the main antibiotic treatments prescribed nowadays.