Helminth-Induced Human Gastrointestinal Dysbiosis: a Systematic Review and Meta-Analysis Reveals Insights into Altered Taxon Diversity and Microbial Gradient Collapse

Coevolutionary interplay: Helminths-trained immunity and its impact on the rise of inflammatory diseases

The gut biome, a complex ecosystem of micro- and macro-organisms, plays a crucial role in human health. A disruption in this evolutive balance, particularly during early life, can lead to immune dysregulation and inflammatory disorders. 'Biome repletion' has emerged as a potential therapeutic approach, introducing live microbes or helminth-derived products to restore immune balance. While helminth therapy has shown some promise, significant challenges remain in optimizing clinical trials. Factors such as patient genetics, disease status, helminth species, and the optimal timing and dosage of their products or metabolites must be carefully considered to train the immune system effectively. We aim to discuss how helminths and their products induce trained immunity as prospective to treat inflammatory and autoimmune diseases. The molecular repertoire of helminth excretory/secretory products (ESPs), which includes proteins, peptides, lipids, and RNA-carrying extracellular vesicles (EVs), underscores their potential to modulate innate immune cells and hematopoietic stem cell precursors. Mimicking natural delivery mechanisms like synthetic exosomes could revolutionize EV-based therapies and optimizing production and delivery of ESP will be crucial for their translation into clinical applications. By deciphering and harnessing helminth-derived products' diverse modes of action, we can unleash their full therapeutic potential and pave the way for innovative treatments.

Nutraceutical supplement slim reshaped colon histomorphology and reduces Mucispirillum schaedleri in obese mice

Introduction

Bioactive compounds and whole foods have emerged as promising interventions to address gut microbiota dysbiosis linked to obesity. Compounds such as berberine and coenzyme Q10 are well-recognized for their roles in managing metabolic syndrome and exerting antioxidant effects, while beet pulp, rich in fiber and antioxidants, enhances gut health through additional prebiotic benefits.

Methods

This study evaluated the effects of a nutraceutical supplement, Slim, on the modulation of gut microbiota in obese mice induced by a high-fat diet.

Results

Our results demonstrated that Slim supplementation significantly improved lipid metabolism, reshaped colon histomorphology, and decreased levels of Mucispirillum schaedleri, which were correlated with VLDL-c and triglycerides.

Discussion

We suggest these effects are driven by a duplibiotic effect, resulting from the synergistic action of the bioactive compounds.

Antimicrobial peptides in nematode secretions - Unveiling biotechnological opportunities for therapeutics and beyond

Gastrointestinal (GI) parasitic nematodes threaten food security and affect human health and animal welfare globally. Current anthelmintics for use in humans and livestock are challenged by continuous re-infections and the emergence and spread of multidrug resistance, underscoring an urgent need to identify novel control targets for therapeutic exploitation. Recent evidence has highlighted the occurrence of complex interplay between GI parasitic nematodes of humans and livestock and the resident host gut microbiota. Antimicrobial peptides (AMPs) found within nematode biofluids have emerged as potential effectors of these interactions. This review delves into the occurrence, structure, and function of nematode AMPs, highlighting their potential as targets for drug discovery and development. We argue that an integrated approach combining advanced analytical techniques, scalable production methods, and innovative experimental models is needed to unlock the full potential of nematode AMPs and pave the way for the discovery and development of sustainable parasite control strategies.

HIV-Helminth Co-Infections and Immune Checkpoints: Implications for Cancer Risk in South Africa

South Africa has the highest HIV prevalence globally, often co-occurring with helminth infections in impoverished regions. The coexistence of these infections leads to immunological interactions, potentially enhancing oncogenesis by upregulating immune checkpoint molecules (ICs) among other effects. Notably, most ICs are overexpressed in cancer and correlated with its progression. Helminth infections trigger Th2-type immunity, increasing immunosuppressive M2 macrophages, regulatory T cells, and associated IC molecules. PD-L2 is reported to contribute to Th2-type immunity induced by helminth infections. Similarly, TIM-3, elevated during chronic viral infections, induces a similar immunosuppressive profile. CTLA-4 and PD-1 impact T-cell function by interacting with CD28, crucial for T-cell function. CD28 is downregulated in chronic infections and cancer. This study investigated the impact of HIV-helminth co-infection on co-stimulatory and co-inhibitory molecule profiles associated with antitumor immunity. Using 78 serum samples collected from March 2020 to May 2021, participants were categorized into uninfected control (no HIV and helminth infections), HIV-infected, helminth-infected, and HIV-helminth co-infected groups. Multiplex immune regulatory molecule assay analysis was conducted. The data were analyzed using multivariate regression analysis and adjusted for confounders (age, gender, BMI, ART, supplements, and other chronic diseases). The uninfected control group was used as the baseline reference group for analysis. HIV-infected individuals had higher PD-1 (adjusted β = 0.12, p = 0.034) and TIM-3 (adjusted β = 23.15, p = 0.052) levels, with the latter showing a trend toward significance. However, lower CD28 levels (adjusted β = -651.95, p = 0.010) were observed. Helminth-infected individuals had higher TIM-3 levels (adjusted β = 20.98, p = 0.020). The co-infected group had higher PD-1 (unadjusted β = 0.18, p = 0.0046) and PD-L2 (adjusted β = 7.95, p = 0.033) levels. A significant decrease in CD28 profile was observed across all infected groups: HIV-infected (adjusted β = -651.95, p = 0.010), helminth-infected (adjusted β = -674.32, p = 0.001), and co-infected (adjusted β = -671.55, p = 0.044). The results suggest that HIV-helminth co-infections alter immune checkpoint markers, potentially increasing cancer risk by promoting an immunosuppressive microenvironment that hinders anti-cancer immunity. CD28's downregulation underscores immune inefficiency in chronic diseases. Addressing these co-infections is crucial for improving HIV care and potentially reducing cancer risks through targeted strategies.

Distinct gut microbiome features characterize Fasciola hepatica infection and predict triclabendazole treatment outcomes in Peruvian patients

Background

Fasciola hepatica, a globally distributed helminth, causes fasciolosis, a disease with significant health and economic impacts. Variability in triclabendazole (TCBZ) efficacy and emerging resistance are remaining challenges. Evidence suggests that the gut microbiome influences host-helminth interactions and is associated with anthelmintic effects, but its association with human F. hepatica infection and TCBZ efficacy is not well understood.

Methods

In this study, we investigated the relationship between Fasciola hepatica infection and the gut microbiome through metagenomic shotgun sequencing of 30 infected and 60 age- and sex-matched uninfected individuals from Peru. Additionally, we performed a longitudinal analysis to evaluate microbiome dynamics in relation to TCBZ treatment response.

Results and discussion

Infection was associated with specific microbial taxonomic and functional features, including higher abundance of Negativibacillus sp900547015, Blautia A sp000285855, and Prevotella sp002299635 species, and enrichment of microbial pathways linked to survival under stress and depletion of pathways for microbial growth. Unexpectedly, we identified that responders to TCBZ treatment (who cleared infection) harbored many microbiome features significantly different relative to non-responders, both before and after treatment. Specifically, the microbiomes of responders had a higher abundance Firmicutes A and Bacteroides species as well as phospholipid synthesis and glucuronidation pathways, while non-responders had higher abundance of Actinobacteria species including several from the Parolsenella and Bifidobacterium genera, and Bifidobacterium shunt and amino acid biosynthesis pathways.

Conclusions

Our findings underscore the impact of helminth infection on gut microbiome and suggest a potential role of gut microbiota in modulating TCBZ efficacy, offering novel insights into F. hepatica-microbiome interactions and paving the way for microbiome-informed treatment approaches.

Rurality and relative poverty drive acquisition of a stable and diverse gut microbiome in early childhood in a non-industrialized setting

There are limited longitudinal data from non-industrialized settings on patterns and determinants of gut bacterial microbiota development in early childhood. We analysed epidemiological data and stool samples collected from 60 children followed from early infancy to 5 years of age in a rural tropical district in coastal Ecuador. Data were collected longitudinally on a wide variety of individual, maternal, and household exposures. Extracted DNA from stool samples were analysed for bacterial microbiota using 16S rRNA gene sequencing. Both alpha and beta diversity indices suggested stable profiles towards 5 years of age. Greater alpha diversity and lower beta diversity were associated with factors typical of rural poverty including low household incomes, overcrowding, and greater agricultural and animal exposures. Consumption of unpasteurized milk was consistently associated with greater alpha diversity indices. Delivery method and antibiotic exposures during pregnancy and early childhood appeared to have limited effects on developmental trajectories of gut microbiota. Infants living in a non-industrialized setting in conditions of greater poverty and typically rural exposures appeared to acquire more rapidly a stable and diverse gut bacterial microbiome during childhood.

Helminths in alternative therapeutics of inflammatory bowel disease

Inflammatory bowel disease (IBD), which includes Crohn's disease and ulcerative colitis, is a nonspecific chronic inflammation of the gastrointestinal tract. Despite recent advances in therapeutics and newer management strategies, IBD largely remains untreatable. Helminth therapy is a promising alternative therapeutic for IBD that has gained some attention in the last two decades. Helminths have immunomodulatory effects and can alter the gut microbiota. The immunomodulatory effects include a strong Th2 immune response, T-regulatory cell response, and the production of regulatory cytokines. Although concrete evidence regarding the efficacy of helminth therapy in IBD is lacking, clinical studies and studies done in animal models have shown some promise. Most clinical studies have shown that helminth therapy is safe and easily tolerable. Extensive work has been done on the whipworm Trichuris, but other helminths, including Schistosoma, Trichinella, Heligmosomoides, and Ancylostoma, have also been explored for pre-clinical and animal studies. This review article summarizes the potential of helminth therapy as an alternative therapeutic or an adjuvant to the existing therapeutic procedures for IBD treatment.

Akkermansia muciniphila: A promising probiotic against inflammation and metabolic disorders

Metabolic disease is a worldwide epidemic that has become a public health problem. Gut microbiota is considered to be one of the important factors that maintain human health by regulating host metabolism. As an abundant bacterium in the host gut, A. muciniphila regulates metabolic and immune functions, and protects gut health. Multiple studies have indicated that alterations in the abundance of A. muciniphila are associated with various diseases, including intestinal inflammatory diseases, obesity, type 2 diabetes mellitus, and even parasitic diseases. Beneficial effects were observed not only in live A. muciniphila, but also in pasteurized A. muciniphila, A. muciniphila-derived extracellular vesicles, outer membrane, and secreted proteins. Although numerous studies have only proven the simple correlation between multiple diseases and A. muciniphila, an increasing number of studies in animal models and preclinical models have demonstrated that the beneficial impacts shifted from correlations to in-depth mechanisms. In this review, we provide a comprehensive view of the beneficial effects of A. muciniphila on different diseases and summarize the potential mechanisms of action of A. muciniphila in the treatment of diseases. We provide a comprehensive understanding of A. muciniphila for improving host health and discuss the perspectives of A. muciniphila in the future studies.

Interplay Between Helminth Infections, Malnutrition, and Gut Microbiota in Children and Mothers from Pemba, Tanzania: Potential of Microbiota-Directed Interventions

BACKGROUND/OBJECTIVES

Despite efforts within the framework of the Sustainable Development Goal to end malnutrition by 2030, malnutrition and soil-transmitted helminth infections persist in sub-Saharan Africa. A significant barrier to success is the inadequate understanding of effective intervention methods. Most research on the gut microbiota's role in health has been conducted in developed countries, leaving a critical gap in knowledge regarding low-income populations. This study addresses this gap by expanding research on the gut microbiota of underprivileged populations to help tackle these public health challenges.

METHODS

We employed 16S rDNA sequencing to assess the bacterial gut microbiota composition of 60 children (mean age: 26.63 ± 6.36 months) and their 58 mothers (mean age: 30.03 ± 6.31 years) in Pemba, with a focus on helminth infection and nutritional status.

RESULTS

Our differential abundance analysis identified bacterial taxa that were significantly negatively associated with both helminth infections and malnutrition, highlighting the potential for microbiota-directed interventions to address these health issues simultaneously. Notably, we identified Akkermansia, Blautia, Dorea, and Odoribacter as promising probiotic candidates for such interventions. In stunted children, positive co-occurrences were observed between Lactobacillus, Prevotella, and Bacteroides, while Escherichia/Shigella displayed negative co-abundance relationships with short-chain fatty acid (SCFA) producers in the gut microbiota. These findings suggest that administering Lactobacillus and SCFA-producing probiotics to children may foster the growth of beneficial bacteria like Prevotella and Bacteroides while reducing the relative abundance of Escherichia/Shigella, potentially enhancing overall health.

CONCLUSIONS

This study underscores the importance of microbiota-directed interventions in children and women of reproductive age as promising strategies, alongside established approaches, for combating helminth infections and malnutrition in vulnerable populations.

Gut-microbiome profiles among Soil-transmitted helminths (STHs) infected Ethiopian children enrolled in the school-based mass deworming program

BACKGROUND

Soil-transmitted helminths (STHs) and mutualistic gut microbes coexist in the gastrointestinal tract. However, limited data exist regarding how STH infections are associated with gut microbiome profiles.

METHOD

We conducted a cross-sectional analysis of baseline data collected in a longitudinal study to identify and explain differences in microbial communities between STH-infected and non-infected Ethiopian school children. We collected 138 stool samples and analyzed them for STH infection using standard direct wet mount and Kato Katz methods. The gut microbiome profiles were characterized using targeted amplicon sequencing of the 16S rRNA gene from the total DNA extracted from the stools.

RESULTS

Children infected with Trichuris trichiura showed significantly lower microbial diversity than those who were non-infected (p<0.05). We also observed significant difference in microbiome composition based on Trichuris trichiura infection status (PERMANOVA p< 0.01). A comparison of microbial taxa at the genus level among participants infected with different helminth species showed a significant increase in Agathobacter relative abundance among children infected with Trichuris trichiura compared to non-infected subjects (adjusted p = 0.001).

CONCLUSIONS

Our results indicate that changes in the gut microbiome composition may vary depending on the species of helminth present. Further studies should investigate how Trichuris trichiura selectively alters microbiome composition compared to other STH species.

Management and Incidence of Enterobius vermicularis Infestation in Appendectomy Specimens: A Cross-Sectional Study of 6359 Appendectomies

Background: The role of Enterobius vermicularis infestation in the context of appendicitis is largely overlooked, but Enterobius vermicularis is considered an unexpected and significant appendicectomy finding. The aim of this study was to investigate the frequency of Enterobius vermicularis findings in appendectomies and to evaluate the clinical and histopathologic features of patients with Enterobius vermicularis-associated acute appendicitis and those with appendiceal Enterobius vermicularis infestation. Methods: The medical records of all children who underwent an appendectomy in two large pediatric centers in Croatia between 1 January 2009 and 1 January 2024 were retrospectively reviewed. Of 6359 appendectomies, 61 (0.96%) children were diagnosed with Enterobius vermicularis on histopathology and included in further analysis. The groups were compared with regard to demographic characteristics, laboratory values, clinical features and histopathological findings. Results: The incidence of enterobiasis fluctuated slightly in the individual study years, but was constant overall. The median age of all patients was 11 years (IQR 8.5, 13), with females predominating (60.7%). Acute appendicitis was observed in 34% of the appendiceal species. The patients with Enterobius vermicularis infestation, without appendicitis, were younger (9 years (IQR 8, 13) vs. 12 years (IQR 10, 15); p = 0.020), had longer duration of symptoms (36 h (IQR, 12, 48) vs. 24 h (IQR, 12, 36); p = 0.034), lower body temperature (37 °C (IQR 36.8, 37.4) vs. 37.6 °C (IQR, 37, 38.6) p = 0.012), lower Appendicitis Inflammation Response (AIR) score (3 (IQR 2, 5) vs. 7 (IQR 5, 9.5) p < 0.001), lower incidence of rebound tenderness (57.1% vs. 20%; p = 0.003) and less frequent vomiting (12.5% vs. 47.6%; p = 0.004) compared to the patients with Enterobius vermicularis-associated acute appendicitis. Acute inflammatory markers in the laboratory showed significantly higher values in the group of patients with acute appendicitis: C-reactive protein (p = 0.009), White blood cells (p = 0.001) and neutrophils (p < 0.001). Eosinophilia was not found in any of the groups, although eosinophil counts were significantly higher in children who had Enterobius vermicularis infestation than in those with Enterobius vermicularis-related appendicitis (2.5% (IQR 0.9, 4.3) vs. 1.8% (IQR 0.7, 2.1); p = 0.040). Conclusions: Pediatric surgeons should consider Enterobius vermicularis infestation as a differential diagnosis when removing a vermiform appendix. Younger age, longer duration of symptoms, lower body temperature, lower AIR score, lower diameter of the appendix and normal laboratory inflammatory markers could predict Enterobius vermicularis infection in children presenting with right iliac fossa pain and avoid unnecessary appendectomy.

Functional characterization of helminth-associated Clostridiales reveals covariates of Treg differentiation

BACKGROUND

Parasitic helminths influence the composition of the gut microbiome. However, the microbiomes of individuals living in helminth-endemic regions are understudied. The Orang Asli, an indigenous population in Malaysia with high burdens of the helminth Trichuris trichiura, display microbiotas enriched in Clostridiales, an order of spore-forming obligate anaerobes with immunogenic properties. We previously isolated novel Clostridiales that were enriched in these individuals and found that a subset promoted the Trichuris life cycle. In this study, we aimed to further characterize the functional properties of these bacteria.

RESULTS

Clostridiales isolates were profiled for their ability to perform 57 enzymatic reactions and produce short-chain fatty acids (SCFAs) and hydrogen sulfide, revealing that these bacteria were capable of a range of activities associated with metabolism and host response. Consistent with this finding, monocolonization of mice with individual isolates identified bacteria that were potent inducers of regulatory T-cell (Treg) differentiation in the colon. Comparisons between variables revealed by these studies identified enzymatic properties correlated with Treg induction and Trichuris egg hatching.

CONCLUSION

We identified Clostridiales species that are sufficient to induce high levels of Tregs. We also identified a set of metabolic activities linked with Treg differentiation and Trichuris egg hatching mediated by these newly isolated bacteria. Altogether, this study provides functional insights into the microbiotas of individuals residing in a helminth-endemic region. Video Abstract.

Modulation of the rat intestinal microbiota in the course of Anisakis pegreffii infection

Background

Anisakis are globally distributed, marine parasitic nematodes that can cause human health problems, including symptoms such as vomiting, acute diarrhea, and allergic reactions. As parasitic nematodes that primarily affect the patient's digestive tract, intestinal helminths can interact directly with the host microbiota through physical contact, chemicals, or nutrient competition. It is widely accepted that the host microbiota plays a crucial role in the regulation of immunity.

Materials and methods

Nematodes collected from the abdominal cavity of marine fish were identified by molecular biology and live worms were artificially infected in rats. Infection was determined by indirect ELISA based on rat serum and worm extraction. Feces were collected for 16S rDNA-based analysis of microbiota diversity.

Results

Molecular biology identification based on ITS sequences identified the collected nematodes as A. pegreffii. The success of the artificial infection was determined by indirect ELISA based on serum and worm extraction from artificially infected rats. Microbiota diversity analysis showed that a total of 773 ASVs were generated, and PCoA showed that the infected group was differentiated from the control group. The control group contained five characterized genera (Prevotellaceae NK3B31 group, Turicibacter, Clostridium sensu stricto 1, Candidatus Stoquefichus, Lachnospira) and the infected group contained nine characterized genera (Rodentibacter, Christensenella, Dubosiella, Streptococcus, Anaeroplasma, Lactococcus, Papillibacter, Desulfovibrio, Roseburia). Based on the Wilcoxon test, four processes were found to be significant: bacterial secretion system, bacterial invasion of epithelial cells, bacterial chemotaxis, and ABC transporters.

Conclusion

This study is the first to analyze the diversity of the intestinal microbiota of rats infected with A. pegreffii and to determine the damage and regulation of metabolism and immunity caused by the infection in the rat gut. The findings provide a basis for further research on host-helminth-microbe correlationships.

Getting around the roundworms: Identifying knowledge gaps and research priorities for the ascarids

The ascarids are a large group of parasitic nematodes that infect a wide range of animal species. In humans, they cause neglected diseases of poverty; many animal parasites also cause zoonotic infections in people. Control measures include hygiene and anthelmintic treatments, but they are not always appropriate or effective and this creates a continuing need to search for better ways to reduce the human, welfare and economic costs of these infections. To this end, Le Studium Institute of Advanced Studies organized a two-day conference to identify major gaps in our understanding of ascarid parasites with a view to setting research priorities that would allow for improved control. The participants identified several key areas for future focus, comprising of advances in genomic analysis and the use of model organisms, especially Caenorhabditis elegans, a more thorough appreciation of the complexity of host-parasite (and parasite-parasite) communications, a search for novel anthelmintic drugs and the development of effective vaccines. The participants agreed to try and maintain informal links in the future that could form the basis for collaborative projects, and to co-operate to organize future meetings and workshops to promote ascarid research.

Eimeria infections of plateau pika altered the patterns of temporal alterations in gut bacterial communities

Intestinal parasites, such as Eimeria, are common among plateau pika (Ochotona curzoniae). The gut microbiome is an essential driver of the host response to gastrointestinal parasites. However, the effects of intestinal protozoal parasites on the temporal variations in the gut microbiome and behavioral and physiological activities remain unknown. Our study conducted treatments involving experimental feeding of pika with Eimeria oocysts or anticoccidia under laboratory conditions to focus on the parasite-associated alterations in gut bacterial communities, host behavioral activity, physiology, and host-bacteria relationships. The results showed insignificant differences in bacterial community structures among treatments on the basis of Bray-Curtis distance metrics, whereas the patterns of temporal alterations in the bacterial communities were changed by the treatments. Bacterial alpha diversities did not vary with the treatments, and experimental feeding with Eimeria slowed down the decrement rate of alpha diversity. Furthermore, few bacterial members were significantly changed by the treatments-only the genus Ruminococcus and the species Ruminococcus flavefaciens, which were associated with energy metabolism. Experimental feeding with Eimeria modified the temporal variations in the bacterial members, including a lower loss rate of the relative abundance of the dominant families Muribaculaceae and Ruminococcaceae in the group with Eimeria experimental feeding. Moreover, a shifting energy trade-off was suggested by the parasite-induced increments in thyroid hormones (triiodothyronine and tetraiodothyronine) and decrements in exploration behavior in the group with Eimeria feeding. However, we did not detect specific connections between gut bacterial communities and pika behaviors and physiology in terms of energy trade-offs. Further in-depth research is needed to examine the role of Eimeria-modified differences in the gut bacteria of plateau pika.

Akkermansia muciniphila: a deworming partner independent of type 2 immunity

The gut microbiota has coevolved with the host for hundreds of millions of years, playing a beneficial role in host health. Human parasitic helminths are widespread and pose a pervasive global public health issue. Although Type 2 immunity provides partial resistance to helminth infections, the composition of the gut microbiota can change correspondingly. Therefore, it raises the question of what role the gut microbiota plays during helminth infection. Akkermansia muciniphila has emerged as a notable representative of beneficial microorganisms in the gut microbiota. Recent studies indicate that A. muciniphila is not merely associated with helminth infection but is also causally linked to infection. Here, we provide an overview of the crosstalk between A. muciniphila and enteric helminth infection. Our goal is to enhance our understanding of the interplay among A. muciniphila, helminths, and their hosts while also exploring the potential underlying mechanisms.

Toxocara canis-induced changes in host intestinal microbial communities

BACKGROUND

Toxocara canis is a roundworm that resides in the gastrointestinal tract of dogs and causes various pathological changes. The dog's intestinal system consists of a diverse and dynamic bacterial community that has extensive effects on intestinal physiology, immunity and metabolics. In the case of intestinal parasites, interactions with the host intestinal flora are inevitable during the process of parasitism.

METHODS

We studied the role of T. canis in regulating the composition and diversity of the intestinal flora of the host by high-throughput sequencing of the 16S ribosomal RNA gene and various bioinformatics analyses.

RESULTS

The α-diversity analysis showed that Toxocara canis infection resulted in a significant decrease in the abundance and diversity of host intestinal flora. The β-diversity analysis showed that the intestinal flora of infected dogs was similar to that carried by T. canis. Analysis of the microflora composition and differences at the phylum level showed that the ratio of Firmicutes to Bacteroidetes (F/B ratio) increased with T. canis infection. Analysis of species composition and differences at the genus level revealed that the proportion of some of the pathogenic bacteria, such as Clostridium sensu stricto and Staphylococcus, increased after T. canis infection.

CONCLUSIONS

Toxocara canis infection affected the composition and diversity of the flora in the host intestinal tract. These results not only shed light on the potential mechanism of T. canis invasion and long-term survival in the intestinal tract, but also provide a new basis for the development of anthelmintic drugs.

Strongyloides stercoralis infection reduces Fusicatenibacter and Anaerostipes in the gut and increases bacterial amino-acid metabolism in early-stage chronic kidney disease

Understanding gut bacterial composition and proteome changes in patients with early-stage chronic kidney disease (CKD) could lead to better methods of controlling the disease progression. Here, we investigated the gut microbiome and microbial functions in patients with S. stercoralis infection (strongyloidiasis) and early-stage CKD. Thirty-five patients with early stages (1-3) of CKD were placed in two groups matched for population characteristics and biochemical parameters, 12 patients with strongyloidiasis in one group and 23 uninfected patients in the other. From every individual, a sample of their feces was obtained and processed for 16S rRNA sequencing and metaproteomic analysis using tandem liquid chromatography-mass spectrometry (LC-MS/MS). Strongyloides stercoralis infection per se did not significantly alter gut microbial diversity. However, certain genera (Bacteroides, Faecalibacterium, Fusicatenibacter, Sarcina, and Anaerostipes) were significantly more abundant in infection-free CKD patients than in infected individuals. The genera Peptoclostridium and Catenibacterium were enriched in infected patients. Among the significantly altered genera, Fusicatenibacter and Anaerostipes were the most correlated with renal parameters. The relative abundance of members of the genus Fusicatenibacter was moderately positively correlated with estimated glomerular filtration rate (eGFR) (r = 0.335, p = 0.049) and negatively with serum creatinine (r = -0.35, p = 0.039). Anaerostipes, on the other hand, showed a near-significant positive correlation with eGFR (r = 0.296, p = 0.084). Individuals with S. stercoralis infection had higher levels of bacterial proteins involved in amino-acid metabolism. Analysis using STITCH predicted that bacterial amino-acid metabolism may also be involved in the production of colon-derived uremic toxin (indole), a toxic substance known to promote CKD. Strongyloides stercoralis infection is, therefore, associated with reduced abundance of Fusicatenibacter and Anaerostipes (two genera possibly beneficial for kidney function) and with increased bacterial amino-acid metabolism in the early-stages of CKD, potentially producing uremic toxin. This study provides useful information for prevention of progression of CKD beyond the early stages.

Meta-Analysis Reveals Compositional and Functional Microbial Changes Associated with Osteoporosis

Over the past decade, the role of the gut microbiota in many disease states has gained a great deal of attention. Mounting evidence from case-control and observational studies has linked changes in the gut microbiota to the pathophysiology of osteoporosis (OP). Nonetheless, the results of these studies contain discrepancies, leaving the literature without a consensus on osteoporosis-associated microbial signatures. Here, we conducted a comprehensive meta-analysis combining and reexamining five publicly available 16S rRNA partial sequence data sets to identify gut bacteria consistently associated with osteoporosis across different cohorts. After adjusting for the batch effect associated with technical variation and heterogeneity of studies, we observed a significant shift in the microbiota composition in the osteoporosis group. An increase in the relative abundance of opportunistic pathogens Clostridium sensu stricto, Bacteroides, and Intestinibacter was observed in the OP group. Moreover, short-chain-fatty-acid (SCFA) producers, including members of the genera Collinsella, Megasphaera, Agathobaculum, Mediterraneibacter, Clostridium XIV, and Dorea, were depleted in the OP group relative to the healthy control (HC) group. Lactic acid-producing bacteria, including Limosilactobacillus, were significantly increased in the OP group. The random forest algorithm further confirmed that these bacteria differentiate the two groups. Furthermore, functional prediction revealed depletion of the SCFA biosynthesis pathway (glycolysis, tricarboxylic acid [TCA] cycle, and Wood-Ljungdahl pathway) and amino acid biosynthesis pathway (methionine, histidine, and arginine) in the OP group relative to the HC group. This study uncovered OP-associated compositional and functional microbial alterations, providing robust insight into OP pathogenesis and aiding the possible development of a therapeutic intervention to manage the disease. IMPORTANCE Osteoporosis is the most common metabolic bone disease associated with aging. Mounting evidence has linked changes in the gut microbiota to the pathophysiology of osteoporosis. However, which microbes are associated with dysbiosis and their impact on bone density and inflammation remain largely unknown due to inconsistent results in the literature. Here, we present a meta-analysis with a standard workflow, robust statistical approaches, and machine learning algorithms to identify notable microbial compositional changes influencing osteoporosis.

Functional characterization of helminth-associated Clostridiales reveals covariates of Treg differentiation

Parasitic helminths influence the composition of the gut microbiome. However, the microbiomes of individuals living in helminth-endemic regions are understudied. The Orang Asli, an indigenous population in Malaysia with high burdens of the helminth Trichuris trichiura, displayed microbiotas enriched in Clostridiales, an order of spore-forming obligate anaerobes previously shown to have immunogenic properties. We previously isolated novel Clostridiales that were enriched in these individuals and found that a subset promoted the Trichuris life cycle. Here, we further characterized the functional properties of these bacteria. Enzymatic and metabolomic profiling revealed a range of activities associated with metabolism and host response. Consistent with this finding, monocolonization of mice with individual isolates identified bacteria that were potent inducers of regulatory T cell (Treg) differentiation in the colon. Comparisons between variables revealed by these studies identified enzymatic properties correlated with Treg induction and Trichuris egg hatching. These results provide functional insights into the microbiotas of an understudied population.

Impact of helminth-microbiome interactions on childhood health and development-A clinical perspective

Humans have co-existed with parasites for virtually the entirety of our existence as a species. Today, nearly one third of the human population is infected with at least one helminthic species, most of which reside in the intestinal tract, where they have co-evolved alongside the human gut microbiota (GM). Appreciation for the interconnected relationship between helminths and GM has increased in recent years. Here, we review the evidence of how helminths and GM can influence various aspects of childhood development and the onset of paediatric diseases. We discuss the emerging evidence of how many of the changes that parasitic worms inflict on their host is enacted through gut microbes. In this light, we argue that helminth-induced microbiota modifications are of great importance in both facing the global challenge of overcoming parasitic infections, and in replicating helminthic protective effects against inflammatory diseases. We propose that deepening our knowledge of helminth-microbiota interactions will uncover novel, safer and more effective therapeutic strategies in combatting an array of childhood disorders.

Gastrointestinal worms and bacteria: From association to intervention

A plethora of studies, both experimental and epidemiological, have indicated the occurrence of associations between infections by gastrointestinal (GI) helminths and the composition and function of the host gut microbiota. Given the worldwide risk and spread of anthelmintic resistance, particularly for GI parasites of livestock, a better understanding of the mechanisms underpinning the relationships between GI helminths and the gut microbiome, and between the latter and host health, may assist the development of novel microbiome-targeting and other bacteria-based strategies for parasite control. In this article, we review current and prospective methods to manipulate the host gut microbiome, and/or to exploit the immune stimulatory and modulatory properties of gut bacteria (and their products) to counteract the negative impact of GI worm infections; we also discuss the potential applications of these intervention strategies in programmes aimed to aid the fight against helminth diseases of humans and livestock.

Chronic Strongyloides stercoralis infection increases presence of the Ruminococcus torques group in the gut and alters the microbial proteome

We explored the impact of chronic Strongyloides stercoralis infection on the gut microbiome and microbial activity in a longitudinal study. At baseline (time-point T0), 42 fecal samples from matched individuals (21 positive for strongyloidiasis and 21 negative) were subjected to microbiome 16S-rRNA sequencing. Those positive at T0 (untreated then because of COVID19 lockdowns) were retested one year later (T1). Persistent infection in these individuals indicated chronic strongyloidiasis: they were treated with ivermectin and retested four months later (T2). Fecal samples at T1 and T2 were subjected to 16S-rRNA sequencing and LC-MS/MS to determine microbial diversity and proteomes. No significant alteration of indices of gut microbial diversity was found in chronic strongyloidiasis. However, the Ruminococcus torques group was highly over-represented in chronic infection. Metaproteome data revealed enrichment of Ruminococcus torques mucin-degrader enzymes in infection, possibly influencing the ability of the host to expel parasites. Metaproteomics indicated an increase in carbohydrate metabolism and Bacteroidaceae accounted for this change in chronic infection. STITCH interaction networks explored highly expressed microbial proteins before treatment and short-chain fatty acids involved in the synthesis of acetate. In conclusion, our data indicate that chronic S. stercoralis infection increases Ruminococcus torques group and alters the microbial proteome.

Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host

BACKGROUND

Intestinal helminths are extremely prevalent among humans and animals. In particular, intestinal roundworms affect more than 1 billion people around the globe and are a major issue in animal husbandry. These pathogens live in intimate contact with the host gut microbiota and harbor bacteria within their own intestines. Knowledge of the bacterial host microbiome at the site of infection is limited, and data on the parasite microbiome is, to the best of our knowledge, non-existent.

RESULTS

The intestinal microbiome of the natural parasite and zoonotic macropathogen, Ascaris suum was analyzed in contrast to the diversity and composition of the infected host gut. 16S sequencing of the parasite intestine and host intestinal compartments showed that the parasite gut has a significantly less diverse microbiome than its host, and the host gut exhibits a reduced microbiome diversity at the site of parasite infection in the jejunum. While the host's microbiome composition at the site of infection significantly determines the microbiome composition of its parasite, microbial signatures differentiate the nematodes from their hosts as the Ascaris intestine supports the growth of microbes that are otherwise under-represented in the host gut.

CONCLUSION

Our data clearly indicate that a nematode infection reduces the microbiome diversity of the host gut, and that the nematode gut represents a selective bacterial niche harboring bacteria that are derived but distinct from the host gut. Video Abstract.

Following the Indian Immigrant: adoption of westernization results in a western gut microbiome and an increased risk of inflammatory bowel diseases

Indians who migrate to westernized countries such as Canada, the USA, and the UK are at an increased risk of developing inflammatory bowel disease (IBD). While the underlying aetiology of IBD remains unclear, a gut microbiome, i.e. no longer symbiotic with its host, is a major player. Increasing IBD incidence in Indian immigrants may be due to the adoption of western practices that result in loss of tolerance of a symbiotic community in the gut and its underlying immune responses. However, little is known about the microbial changes in the Indian gut, including shifts in the microbiome when they migrate to westernized countries. In this Current Opinion, we discuss what is known about the Indian gut microbiome and how living in a westernized environment may be impeding what was once a symbiotic relationship with their gut microbiome and intestinal mucosae, which may be the driving factor in their increased risk of IBD.

Clostridia isolated from helminth-colonized humans promote the life cycle of Trichuris species

Soil-transmitted intestinal worms known as helminths colonize over 1.5 billion people worldwide. Although helminth colonization has been associated with altered composition of the gut microbiota, such as increases in Clostridia, individual species have not been isolated and characterized. Here, we isolate and sequence the genome of 13 Clostridia from the Orang Asli, an indigenous population in Malaysia with a high prevalence of helminth infections. Metagenomic analysis of 650 fecal samples from urban and rural Malaysians confirm the prevalence of species corresponding to these isolates and reveal a specific association between Peptostreptococcaceae family members and helminth colonization. Remarkably, Peptostreptococcaceae isolated from the Orang Asli display superior capacity to promote the life cycle of whipworm species, including hatching of eggs from Trichuris muris and Trichuris trichiura. These findings support a model in which helminths select for gut colonization of microbes that support their life cycle.

Immunomodulatory and biological properties of helminth-derived small molecules: Potential applications in diagnostics and therapeutics

Parasitic helminths secrete and excrete a vast array of molecules known to help skew or suppress the host's immune response, thereby establishing a niche for sustained parasite maintenance. Indeed, the immunomodulatory potency of helminths is attributed mainly to excretory/secretory products (ESPs). The ESPs of helminths and the identified small molecules (SM) are reported to have diverse biological and pharmacological properties. The available literature reports only limited metabolites, and the identity of many metabolites remains unknown due to limitations in the identification protocols and helminth-specific compound libraries. Many metabolites are known to be involved in host-parasite interactions and pathogenicity. For example, fatty acids (e.g., stearic acid) detected in the infective stages of helminths are known to have a role in host interaction through facilitating successful penetration and migration inside the host. Moreover, excreted/secreted SM detected in helminth species are found to possess various biological properties, including anti-inflammatory activities, suggesting their potential in developing immunomodulatory drugs. For example, helminths-derived somatic tissue extracts and whole crude ESPs showed anti-inflammatory properties by inhibiting the secretion of proinflammatory cytokines from human peripheral blood mononuclear cells and suppressing the pathology in chemically-induced experimental mice model of colitis. Unlike bigger molecules like proteins, SM are ideal candidates for drug development since they are small structures, malleable, and lack immunogenicity. Future studies should strive toward identifying unknown SM and isolating the under-explored niche of helminth metabolites using the latest metabolomics technologies and associated software, which hold potential keys for finding new diagnostics and novel therapeutics.

Effects of helminths on the human immune response and the microbiome

Helminths have evolved sophisticated immune regulating mechanisms to prevent rejection by their mammalian host. Our understanding of how the human immune system responds to these parasites remains poor compared to mouse models of infection and this limits our ability to develop vaccines as well as harness their unique properties as therapeutic strategies against inflammatory disorders. Here, we review how recent studies on human challenge infections, self-infected individuals, travelers, and endemic populations have improved our understanding of human type 2 immunity and its effects on the microbiome. The heterogeneity of responses between individuals and the limited access to tissue samples beyond the peripheral blood are challenges that limit human studies on helminths, but also provide opportunities to transform our understanding of human immunology. Organoids and single-cell sequencing are exciting new tools for immunological analysis that may aid this pursuit. Learning about the genetic and immunological basis of resistance, tolerance, and pathogenesis to helminth infections may thus uncover mechanisms that can be utilized for therapeutic purposes.

Detangling the Crosstalk Between Ascaris, Trichuris and Gut Microbiota: What´s Next?

Helminth infections remain a global public health issue, particularly in low- and middle-income countries, where roundworms from theTrichuris and Ascaris genera are most prevalent. These geohelminths not only impact human health but most importantly also affect animal well-being, in particular the swine industry. Host-helminth parasite interactions are complex and at the same time essential to understand the biology, dynamics and pathophysiology of these infections. Within these interactions, the immunomodulatory capacity of these helminths in the host has been extensively studied. Moreover, in recent years a growing interest on how helminths interact with the intestinal microbiota of the host has sparked, highlighting how this relationship plays an essential role in the establishment of initial infection, survival and persistence of the parasite, as well as in the development of chronic infections. Identifying the changes generated by these helminths on the composition and structure of the host intestinal microbiota constitutes a field of great scientific interest, since this can provide essential and actionable information for designing effective control and therapeutic strategies. Helminths like Trichuris and Ascaris are a focus of special importance due to their high prevalence, higher reinfection rates, resistance to anthelmintic therapy and unavailability of vaccines. Therefore, characterizing interactions between these helminths and the host intestinal microbiota represents an important approach to better understand the nature of this dynamic interface and explore novel therapeutic alternatives based on management of host microbiota. Given the extraordinary impact this may have from a biological, clinical, and epidemiological public health standpoint, this review aims to provide a comprehensive overview of current knowledge and future perspectives examining the parasite-microbiota interplay and its impact on host immunity.

Worms and bugs of the gut: the search for diagnostic signatures using barcoding, and metagenomics-metabolomics

Gastrointestinal (GI) helminth infections cause significant morbidity in both humans and animals worldwide. Specific and sensitive diagnosis is central to the surveillance of such infections and to determine the effectiveness of treatment strategies used to control them. In this article, we: (i) assess the strengths and limitations of existing methods applied to the diagnosis of GI helminth infections of humans and livestock; (ii) examine high-throughput sequencing approaches, such as targeted molecular barcoding and shotgun sequencing, as tools to define the taxonomic composition of helminth infections; and (iii) discuss the current understanding of the interactions between helminths and microbiota in the host gut. Stool-based diagnostics are likely to serve as an important tool well into the future; improved diagnostics of helminths and their environment in the gut may assist the identification of biomarkers with the potential to define the health/disease status of individuals and populations, and to identify existing or emerging anthelmintic resistance.

Possible Interactions between Malaria, Helminthiases and the Gut Microbiota: A Short Review

Malaria, caused by the Plasmodium species, is an infectious disease responsible for more than 600 thousand deaths and more than 200 million morbidity cases annually. With above 90% of those deaths and cases, sub-Saharan Africa is affected disproportionately. Malaria clinical manifestations range from asymptomatic to simple, mild, and severe disease. External factors such as the gut microbiota and helminthiases have been shown to affect malaria clinical manifestations. However, little is known about whether the gut microbiota has the potential to influence malaria clinical manifestations in humans. Similarly, many previous studies have shown divergent results on the effects of helminths on malaria clinical manifestations. To date, a few studies, mainly murine, have shown the gut microbiota’s capacity to modulate malaria’s prospective risk of infection, transmission, and severity. This short review seeks to summarize recent literature about possible interactions between malaria, helminthiases, and the gut microbiota. The knowledge from this exercise will inform innovation possibilities for future tools, technologies, approaches, and policies around the prevention and management of malaria in endemic countries.