Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota

Transient colonization with Blastocystis spp. after transmission via fecal microbiota transplantation

BACKGROUND

The pathogenicity of Blastocystis spp. is still debated. Guidelines for feces donor screening differ in their advice to screen for Blastocystis spp., but when tested, its presence is a common reason for exclusion. Blastocystis spp. are correlated to increased bacterial alpha-diversity and distinct bacterial groups and therefore its presence may indicate favorable efficacy of fecal microbiota transplantation (FMT). The latest European consensus report no longer advices rejecting feces donors testing positive for Blastocystis spp. Only one paper has been published on human transmission of Blastocystis spp. via frozen FMT.

OBJECTIVE

To investigate the transmission and long-term effects of Blastocystis-positive FMT, prepared with fresh (i.e., unfrozen) feces.

METHODS

In a trial (NCT03074227) on FMT for refractory Irritable Bowel Syndrome (IBS), adolescents (age 16-20 years) received two administrations - at baseline and after 6 weeks - of fresh allogeneic FMT from a Blastocystis-positive donor via nasoduodenal tube. The follow-up was 48 weeks. Blastocystis spp. presence, viability and subtyping were determined using microscopy, culture, PCR and sequencing.

RESULTS

Three recipients received FMT from one donor colonized with Blastocystis subtype 3 (ST3). At baseline, two recipients were negative for Blastocystis spp. and one recipient carried ST2. Culturing revealed viable Blastocystis spp. in fresh donor feces but not in frozen samples. After FMT with fresh feces, the two prior-negative recipients tested positive for the donor's ST3 at 12 weeks, but had lost this subtype by week 24 and 48. The recipient initially colonized with ST2 remained colonized with ST2 and did not acquire ST3. Transient adverse events occurred, but did not differ from patients treated with Blastocystis-negative FMT. No FMT-related serious adverse events emerged.

CONCLUSION

We present the first long-term data on viable Blastocystis spp. transmission via fresh FMT in three cases. Transient colonization with Blastocystis spp. was observed, without serious FMT-related adverse events.

Decoding Blastocystis-Driven Mechanisms in Gut Microbiota and Host Metabolism

Blastocystis, a prevalent eukaryotic microorganism in the gut microbiota, has emerged as a potential link between healthy diets and improved cardiometabolic health. Despite its genetic diversity and varied host interactions, Blastocystis is consistently associated with healthier dietary patterns and reduced risk of cardiometabolic diseases. Current evidence suggests that Blastocystis may influence host metabolism by modulating gut microbial composition, short-chain fatty acids (SCFAs) production, and immune cell differentiation. Moreover, its role in tryptophan metabolism provides intriguing insights into its potential impact on host signaling pathways. However, mechanistic evidence connecting Blastocystis to improved metabolic health remains limited. This perspective explores plausible pathways, including SCFAs-mediated signaling, tryptophan metabolism, and immune modulation, through which Blastocystis may exert its effects. A systematic research framework integrating axenic cultivation, in vitro co-culture systems, animal models, and multi-omics approaches is proposed to further elucidate these mechanisms and expand the understanding of Blastocystis in gut health and disease.

Microbiota in inflammatory bowel disease: mechanisms of disease and therapeutic opportunities

Perturbations in the intestinal microbiome are strongly linked to the pathogenesis of inflammatory bowel disease (IBD). Bacteria, fungi and viruses all make up part of a complex multi-kingdom community colonizing the gastrointestinal tract, often referred to as the gut microbiome. They can exert various effects on the host that can contribute to an inflammatory state. Advances in screening, multiomics and experimental approaches have revealed insights into host-microbiota interactions in IBD and have identified numerous mechanisms through which the microbiota and its metabolites can exert a major influence on the gastrointestinal tract. Looking into the future, the microbiome and microbiota-associated processes will be likely to provide unparalleled opportunities for novel diagnostic, therapeutic and diet-inspired solutions for the management of IBD through harnessing rationally designed microbial communities, powerful bacterial and fungal metabolites, individually or in combination, to foster intestinal health. In this Review, we examine the current understanding of the cross-kingdom gut microbiome in IBD, focusing on bacterial and fungal components and metabolites. We examine therapeutic and diagnostic opportunities, the microbial metabolism, immunity, neuroimmunology and microbiome-inspired interventions to link mechanisms of disease and identify novel research and therapeutic opportunities for IBD.

Exploring the complex interplay of Blastocystis, morbid obesity, and bariatric surgery on gut microbial dynamics

This study examines Blastocystis dynamics in 15 individuals undergoing sleeve gastrectomy. Molecular detection involved DNA extraction, RT-PCR, and sequencing, while 16S rRNA sequencing via Illumina MiSeq analyzed the intestinal microbiome. Statistical analysis through SPSS considered a significance level of p < 0.05. Postoperative colonization of Blastocystis was observed in previously negative individuals, revealing subtypes and shifts in microbial taxa. Blastocystis-positive participants post-bariatric surgery showed a significant increase in Lachnospira, alongside higher abundances of Bacteroides, Oscillospira, Barnesiellaceae, and Rikenellaceae, with reduced Lactobacillus levels compared to Blastocystis-negative individuals. Collective analysis highlighted higher Clostridiales and RF32 in Blastocystis-positive post-surgery individuals, coupled with decreased Enterobacteriaceae. The study challenges previous notions, suggesting a complex interplay between Blastocystis, morbid obesity, and bariatric surgery. Despite limitations, including small sample sizes and absent gut microbiome diversity comparisons, this pioneering research calls for further investigation into the intricate mechanisms and implications for metabolic health. This study is registered at clinicaltrials.gov (NCT05085769).

Epidemiology of Blastocystis in farm animals: A review

Blastocystis is a ubiquitous gastrointestinal protozoan parasite found both in humans and animals. The purpose of this review is to look at the prevalence and genetic diversity of Blastocystis in farm animals, including cattle, sheep, goats, pigs, and poultry, and discuss the potential evidence of transmission between animals and humans, as well as highlight the related risk factors and public health significance. Significant differences have been found in the prevalence of Blastocystis in different hosts worldwide. The global prevalence of Blastocystis infection was 13.6 % in cattle (1219/8961), 15.9 % in sheep (675/4233), 31.7 % in goats (837/2640), 44.57 % in pigs (2589/5808), and 26.29 % in poultry (892/3392). Blastocystis is mainly transmitted through fecal-oral routes. The existence of the same subtypes of the parasite in both animals and humans indicates potential zoonotic transmission. Subtypes ST10 (43.39 %) and ST14 (19.99 %) were most frequently found in cattle, sheep, and goats, while ST5 (62.57 %) was predominantly observed in pigs, and ST6 (16 %) and ST7 (36.6 %) were commonly recorded in poultry. Analysis of risk factors suggests that age, sex, close contact with animals, geographical location, farm management system, and season were the significant risk factors reported in many studies. Although epidemiology and subtype distribution of Blastocystis in different hosts have been described in several studies, understanding the possible transmission pathway from farm animals to humans and the public health impacts of Blastocystis requires more extensive studies.

Intragenomic diversity of the small subunit rDNA gene shows limited impact on the pathogenicity of Blastocystis infection in clinical patients

The clinical significance of Blastocystis sp. remains to be fully elucidated. This study assesses whether Blastocystis subtype diversity can affect the outcome of the infection and the occurrence of clinical manifestations in infected individuals. Stool samples from 219 Blastocystis-positive patients by PCR targeting the ssu rDNA gene were fully genotyped by Sanger sequencing analyses. Co-infections by other parasitic, viral, and bacterial enteropathogens were identified by molecular and culture methods. Sequence analyses revealed the presence of six Blastocystis subtypes including ST1 (21.5 %), ST2 (17.8 %), ST3 (29.7 %), ST4 (22.8 %), ST6 (5.5 %), and ST7 (2.3 %), with a single sample harbouring a ST1+ST3 co-infection (0.5 %). Multivariate risk factor analyses using logistic regression models indicated that neither Blastocystis subtypes nor patient-associated variables including sex, country of origin, travelling history, and presence of nonspecific symptoms were positively associated with a higher likelihood of developing gastrointestinal symptoms (abdominal pain and diarrhoea). However, being of a young age (p-value: 0.003) and experiencing skin pruritus (p-value < 0.001) and eosinophilia (p-value: 0.016) were found to increase the odds of presenting gastrointestinal symptoms. Blastocystis subtypes based on variability within the ssu rDNA gene do not seem to be the main drivers of clinical manifestations in the surveyed clinical population.

Pitfalls in gut single-cell eukaryote research

Gut single-celled eukaryotes (GSCEs) are found in billions of people worldwide, but we still know little about their functions and relationships in human gut ecology. Lately, retrospective analysis of bacterial data obtained by next-generation sequencing (NGS) methods has been used to identify links between GSCEs, gut bacteria, host metabolism, and host phenotypical traits, suggesting possible direct or indirect associations to favorable gut microbiome features and other health parameters. Here, we highlight some of the pitfalls related to the research strategy typically used so far and propose action points that could pave the way for a more accurate understanding of GSCEs in human health and disease.

Eukaryotic composition across seasons and social groups in the gut microbiota of wild baboons

Background

Animals coexist with complex microbiota, including bacteria, viruses, and eukaryotes (e.g., fungi, protists, and helminths). While the composition of bacterial and viral components of animal microbiota are increasingly well understood, eukaryotic composition remains neglected. Here we characterized eukaryotic diversity in the microbiomes in wild baboons and tested the degree to which eukaryotic community composition was predicted by host social group membership, sex, age, and season of sample collection.

Results

We analyzed a total of 75 fecal samples collected between 2012 and 2014 from 73 wild baboons in the Amboseli ecosystem in Kenya. DNA from these samples was subjected to shotgun metagenomic sequencing, revealing members of the kingdoms Protista, Chromista, and Fungi in 90.7%, 46.7%, and 20.3% of samples, respectively. Social group membership explained 11.2% of the global diversity in gut eukaryotic species composition, but we did not detect statistically significant effect of season, host age, and host sex. Across samples, the most prevalent protists were Entamoeba coli (74.66% of samples), Enteromonas hominis (53.33% of samples), and Blastocystis subtype 3 (38.66% of samples), while the most prevalent fungi included Pichia manshurica (14.66% of samples), and Ogataea naganishii (6.66% of samples).

Conclusions

Protista, Chromista, and Fungi are common members of the gut microbiome of wild baboons. More work on eukaryotic members of primate gut microbiota is essential for primate health monitoring and management strategies.

Metabarcoding in gut protozoology

Next-generation sequencing (NGS) methods include whole-genome sequencing, metagenomic analysis, and amplicon-based NGS, all of which are gaining territory in parasitology. A modality of particular interest within the field of gut protozoology is exhaustive metabarcoding of ribosomal genes in a complex matrix such as faeces, by which method, amplicon-based NGS enables the detection and differentiation of both eukaryotic and prokaryotic organisms, circumventing Sanger sequencing-based limitations and representing a one-fits-most approach. Apart from being a tool to break the code of intracellular genetic variation and tell mixed species infections apart, metabarcoding can produce data that can serve to augment our understanding of the interplay between the organisms within the gut.

Investigation of gut microbiota composition in humans carrying blastocystis subtypes 1 and 2 and Entamoeba hartmanni

The composition of human gut microbiota is dominated by bacteria which have been extensively studied. The role of intestinal eukaryote microorganisms like Blastocystis, however, remains under investigation. Moreover, the potential impact on gut health related to Blastocystis presence was primarily investigated in symptomatic individuals mainly from industrialized countries, and appears to be mostly beneficial to the host microbiota. Data from surveys conducted in underdeveloped countries with higher prevalence and from asymptomatic individuals could therefore be valuable. The aim of this preliminary study was to analyze the composition of the gut microbiota in relation to the protozoa Blastocystis ST1 and ST2 and Entamoeba hartmanni carriage in asymptomatic subjects living in a semi-urban area of Côte d'Ivoire to add data into the ongoing debate on the role of Blastocystis in host health. The amplification of the V3 and V4 regions of bacterial 16S rDNA genes was performed to obtain the gut microbiota composition, and differential analyses on alpha and beta diversity were performed from the phylum to genus taxonomic level. The analysis revealed that individuals positive for both protozoa exhibited higher alpha and beta diversity compared to those who tested negative. Additionally, their bacterial composition showed a reduction in Bacteroides and an increase in Prevotella 9. Relative abundances of some OTUs, particularly Faecalibacterium, observed in individuals who tested positive for protozoa, were correlated with a good state of health of the gut microbiota. Blastocystis ST1 and ST2 associated with E. hartmanni thus appeared to be related to a state of intestinal eubiosis.

Gut microbiome and NAFLD: impact and therapeutic potential

Non-Alcoholic Fatty Liver Disease (NAFLD) affects approximately 32.4% of the global population and poses a significant health concern. Emerging evidence underscores the pivotal role of the gut microbiota-including bacteria, viruses, fungi, and parasites-in the development and progression of NAFLD. Dysbiosis among gut bacteria alters key biological pathways that contribute to liver fat accumulation and inflammation. The gut virome, comprising bacteriophages and eukaryotic viruses, significantly shapes microbial community dynamics and impacts host metabolism through complex interactions. Similarly, gut fungi maintain a symbiotic relationship with bacteria; the relationship between gut fungi and bacteria is crucial for overall host health, with certain fungal species such as Candida in NAFLD patients showing detrimental associations with metabolic markers and liver function. Additionally, the "hygiene hypothesis" suggests that reduced exposure to gut parasites may affect immune regulation and metabolic processes, potentially influencing conditions like obesity and insulin resistance. This review synthesizes current knowledge on the intricate interactions within the gut microbiota and their associations with NAFLD. We highlight the therapeutic potential of targeting these microbial communities through interventions such as probiotics, prebiotics, and fecal microbiota transplantation. Addressing the complexities of NAFLD requires comprehensive strategies that consider the multifaceted roles of gut microorganisms in disease pathology.

Blastocystis hominis; Friend or Foe

Blastocystis hominis (B. hominis) remains the most common parasite identified through stool examination. A clinician will undoubtedly encounter the presence of this parasite numerous times in their career. Thus, it is vital to know if this organism is a 'friend or foe', or in other words, whether it is a commensal or a pathogen. This will help clinicians decide whether to treat or not. This literature review discusses the best available evidence of the association of B. hominis and two diseases- irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). Particularly, focus has been paid to the effect of antimicrobial therapy in improving disease activity/symptoms and concluding on the pathogenicity of B. hominis based on in vitro, observational studies, and randomized controlled trials. Most importantly, the review presents a concise set of recommendations for when and how to treat B. hominis in a patient presenting gastrointestinal ailments.

Gut Microbiota Features in Relation to Fecal Microbiota Transplantation Outcome in Ulcerative Colitis: A Systematic Review and Meta-Analysis

BACKGROUND & AIMS

Fecal microbiota transplantation (FMT) can induce remission in patients with ulcerative colitis, yet its efficacy needs improvement. We conducted a comprehensive evaluation of the current literature on microbial factors affecting outcome, as well as a meta-analysis on some of the largest datasets regarding composition.

METHODS

MEDLINE, Embase, and Cochrane were systematically searched through August 2024 for relevant studies. The quality of studies was analyzed with JBI tools and a composite critical appraisal score. Additionally, species-level data from 2 landmark FMT trials (the Transplantation of Feces in Ulcerative Colitis; Returning Nature's Homeostasis [TURN] and Fecal Microbiota Transplantation for Chronic Active Ulcerative Colitis [FOCUS] trials) were reanalyzed from a compositional perspective.

RESULTS

Out of 3755 citations identified, 56 met the inclusion criteria, of which 29 fulfilled quality standards. Higher microbial α-diversity, either in donors or recipients (at baseline or following FMT treatment), was associated with better clinical response rates. Engraftment of the donors' microbiota could not be clearly linked with clinical response, possibly because not every donor has an ideal microbiome. Butyrate-producing species from the Lachnospiraceae and Oscillospiraceae families were often related with response, whereas the reverse was true for Fusobacteria, many Proteobacteria, and Ruminococcus gnavus. Compositional analyses showed that clinical response is associated with a shift from a low-diversity, often Bacteroides-dominant composition to one with higher diversity, either dominated by various butyrate producers, the Christensenellaceae-Methanobrevibacter trophic network, or a moderate/high-diversity composition with abundant but not excessive levels of Prevotella copri.

CONCLUSIONS

This systematic review/meta-analysis yielded a coherent picture from a compositional perspective, which may help identify beneficial donor profiles and guide personalized FMT approaches.

Metagenomic discovery of microbial eukaryotes in stool microbiomes

Host-associated microbiota form complex microbial communities that are increasingly associated with host behavior and disease. While these microbes include bacterial, archaeal, viral, and eukaryotic constituents, most studies have focused on bacteria due to their dominance in the human host and available tools for investigation. Accumulating evidence suggests microbial eukaryotes in the microbiome play pivotal roles in host health, but our understandings of these interactions are limited to a few readily identifiable taxa because of technical limitations in unbiased eukaryote exploration. Here, we combined cell sorting, optimized eukaryotic cell lysis, and shotgun sequencing to accelerate metagenomic discovery and analysis of host-associated microbial eukaryotes. Using synthetic communities with a 1% microbial eukaryote representation, the eukaryote-optimized cell lysis and DNA recovery method alone yielded a 38-fold increase in eukaryotic DNA. Automated sorting of eukaryotic cells from stool samples of healthy adults increased the number of microbial eukaryote reads in metagenomic pools by up to 28-fold compared to commercial kits. Read frequencies for identified fungi increased by 10,000× on average compared to the Human Microbiome Project and allowed for the identification of novel taxa, de novo assembly of contigs from previously unknown microbial eukaryotes, and gene prediction from recovered genomic segments. These advances pave the way for the unbiased inclusion of microbial eukaryotes in deciphering determinants of health and disease in the host-associated microbiome.IMPORTANCEMicrobial eukaryotes are common constituents of the human gut where they can contribute to local ecology and host health, but they are often overlooked in microbiome studies. The lack of attention is due to current technical limitations that are heavily biased or poorly recovered DNA from microbial eukaryotes. We developed a method to increase the representation of these eukaryotes in metagenomic sequencing of microbiome samples that allows to improve their detection compared to prior methods and allows for the identification of new species. Application of the technique to gut microbiome samples improved detection of fungi, protists, and helminths. New eukaryotic taxa and their encoded genes could be identified by sequencing a small number of samples. This approach can improve the inclusion of eukaryotes into microbiome research.

Blastocystis occurrence and subtype diversity in European wild boar (Sus scrofa) from the Iberian Peninsula

The ongoing increase in wild boar populations across Europe has fostered human-wildlife conflicts, including the transmission of emerging pathogens with zoonotic importance. Blastocystis is a ubiquitous, faecal-oral transmitted protist that can cause gastrointestinal illnesses and is observed in humans and animals worldwide. The role of wildlife in the epidemiology of Blastocystis is insufficiently understood. Thus, we investigated the occurrence and subtype diversity of Blastocystis in free-ranging wild boars from the Iberian Peninsula using conventional PCR and next-generation amplicon sequencing of a fragment of the ssu RNA gene. A total of 459 wild boar faecal samples were collected across Spain (n = 360) and Portugal (n = 99) between 2014 and 2021. Blastocystis was present in 15.3% (70/459; 95% CI 12.1-18.9) of the wild boars analysed, and its occurrence was significantly higher in Portugal (34.3%, 34/99; 95% CI 25.1-44.6) than in Spain (10.0%, 36/360; 95% CI 7.1-13.6). Seven Blastocystis subtypes (ST5, ST10b, ST13-ST15, ST24b, and ST43) were detected among the surveyed wild boar populations, with greater variability detected in Portuguese samples. ST5 was identified in all the Blastocystis-positive animals, whereas 14.3% of them harboured ST mixed colonisations. Our results demonstrate that Blastocystis ST5 is particularly adapted to infect wild boars. The additional identification of zoonotic STs reinforces the role of wild boars as spreaders of zoonotic infections with public health significance.

Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries

Diet impacts human health, influencing body adiposity and the risk of developing cardiometabolic diseases. The gut microbiome is a key player in the diet-health axis, but while its bacterial fraction is widely studied, the role of micro-eukaryotes, including Blastocystis, is underexplored. We performed a global-scale analysis on 56,989 metagenomes and showed that human Blastocystis exhibits distinct prevalence patterns linked to geography, lifestyle, and dietary habits. Blastocystis presence defined a specific bacterial signature and was positively associated with more favorable cardiometabolic profiles and negatively with obesity (p < 1e-16) and disorders linked to altered gut ecology (p < 1e-8). In a diet intervention study involving 1,124 individuals, improvements in dietary quality were linked to weight loss and increases in Blastocystis prevalence (p = 0.003) and abundance (p < 1e-7). Our findings suggest a potentially beneficial role for Blastocystis, which may help explain personalized host responses to diet and downstream disease etiopathogenesis.

Unlocking the mind-gut connection: Impact of human microbiome on cognition

This perspective explores the current understanding of the gut microbiota's impact on cognitive function in apparently healthy humans and in individuals with metabolic disease. We discuss how alterations in gut microbiota can influence cognitive processes, focusing not only on bacterial composition but also on often overlooked components of the gut microbiota, such as bacteriophages and eukaryotes, as well as microbial functionality. We examine the mechanisms through which gut microbes might communicate with the central nervous system, highlighting the complexity of these interactions. We provide a comprehensive overview of the emerging field of microbiota-gut-brain interactions and its significance for cognitive health. Additionally, we summarize novel therapeutic strategies designed to promote cognitive resilience and reduce the risk of cognitive disorders, focusing on interventions that target the gut microbiota. An in-depth understanding of the microbiome-brain axis is imperative for developing innovative treatments aimed at improving cognitive health.

Intestinal microbiota analysis of different Blastocystis subtypes and Blastocystis-negative individuals in Taiwan

BACKGROUND

Intestinal parasitic infections are the most common infectious diseases among Southeast Asian migrant workers in Taiwan, especially for infections with Blastocystis hominis. However, little is known about the impact of Blastocystis subtypes (STs) on the gut microbiota.

METHODS

We retrospectively evaluated the prevalence of intestinal parasites in a teaching hospital in Northern Taiwan in the period of 2015-2019. Blastocystis-positive stool specimens were collected for ST analysis by polymerase chain reaction in 2020. Intestinal microbiota analyses of different Blastocystis STs and Blastocystis-free individuals were conducted by 16S rRNA sequencing.

RESULTS

A total of 13,859 subjects were analyzed, of which 1802 cases (13%) were diagnosed with intestinal parasitic infections. B. hominis infections were the most prevalent (n = 1546, 85.7%). ST analysis of Blastocystis-positive samples (n = 150) indicated that ST1 was the most common type, followed by ST3, ST4, ST2, ST7, and ST5. Different Blastocystis STs (ST1, ST3, and ST4) were associated with distinct richness and diversity of the microbiota. Taxonomic profiles revealed that Akkermansia muciniphila was significantly enriched for all analyzed Blastocystis STs, whereas Holdemanella biformis was more abundant in the Blastocystis-free group. Additionally, Succinivibrio dextrinosolvens and Coprococcus eutactus were specifically more abundant in ST3 carriers than in non-infected individuals.

CONCLUSION

This study demonstrates that A. muciniphila is positively associated with all Blastocystis STs, while H. biformis was negatively associated with them. Several bacteria were enriched in specific STs, highlighting the need for further microbiota analysis at the ST level to elucidate the pathogenicity of Blastocystis.

Unveiling Blastocystis epidemiology in Morocco: subtype diversity among clinical patients with and without gastrointestinal manifestations in the Meknes region

Blastocystis is an intestinal protist frequently identified in humans and other animals, though its clinical significance remains controversial. This study aimed to determine the prevalence and genetic diversity of Blastocystis in faecal samples from symptomatic (n = 55) and asymptomatic (n = 50) individuals seeking medical care in Meknes, Morocco. Detection of the protist was accomplished through coproparasitological examination and culture in Jones medium. Culture-positive samples were subjected to molecular analyses (PCR and Sanger sequencing) based on sequences of the small subunit ribosomal RNA gene. Epidemiological questionnaires on demographics and potential risk factors were collected from participating patients. The overall Blastocystis infection rate was 51.4% (54/105), with no differences between symptomatic (52.7%, 29/55) and asymptomatic (50.0%, 25/50) individuals. Sequence analyses identified three Blastocystis subtypes, with ST3 being the most prevalent (42.0%), followed by ST1 (34.0%), and ST2 (12.0%). Regarding intra-subtype diversity, allele 4 was found within ST1; alleles 11/12 and alleles 34/36 (alone or in combination) were identified within ST2 and ST3 respectively. Allele 34 in ST3 (40.8%) and allele 4 in ST1 (34.7%) were the most common genetic variants circulating in the surveyed clinical population. A statistically significant association between ST2 and the presence of flatulence was observed. This is the first study assessing the epidemiology and genetic diversity of Blastocystis sp. in the Meknes region, Morocco.

Blastocystis colonization and associations with population parameters in Thai adults

BACKGROUND

Blastocystis is a unicellular eukaryote commonly found in the intestinal tract of humans and other animals. The prevalence of Blastocystis has been investigated in both developed and developing countries, yet its occurrence and distribution in rural locations has been less studied. Herein, we aimed to examine the distribution of Blastocystis colonization in Thai adults representing background populations along a rural/peri-urban gradient, as well as associations between colonization and personal characteristics.

METHODOLOGY

A total of 238 participants were recruited from rural and peri-urban areas situated in three provinces. The presence of Blastocystis in feces was evaluated using PCR and qPCR. Information on gender, age, region (province), rural/peri-urban location, and body mass index (BMI) was collected.

PRINCIPAL FINDINGS

The overall rate of Blastocystis carriage was 67.2%. Univariate analysis revealed significant associations between Blastocystis carriage and region (p<0.05), location (p<0.001) and age group (p<0.05). Logistic regression analysis revealed that rural/peri-urban location and BMI were significantly associated with Blastocystis carriage. Nine subtypes (ST1-ST7, ST10 and ST23) were identified with ST3, ST7 and ST1 as the most abundant ones, in this order. The greatest diversity of subtypes, in terms of numbers, was found in the middle aged group (nine subtypes), while the least diversity was found in the young adult and obese (three subtypes each) groups.

CONCLUSIONS

This study increases the understanding of the epidemiology of Blastocystis colonization and its association with population parameters and characteristics in middle-income countries.

Large-Scale Molecular Epidemiological Survey of Blastocystis sp. among Herbivores in Egypt and Assessment of Potential Zoonotic Risk

Given the proven zoonotic potential of the intestinal protozoan Blastocystis sp., a fast-growing number of surveys are being conducted to identify potential animal reservoirs for transmission of the parasite. Nevertheless, few epidemiological studies have been conducted on farmed animals in Egypt. Therefore, a total of 1089 fecal samples were collected from herbivores (sheep, goats, camels, horses, and rabbits) in six Egyptian governorates (Dakahlia, Gharbia, Kafr El Sheikh, Giza, Aswan, and Sharqia). Samples were screened for the presence of Blastocystis sp. by real-time PCR followed by sequencing of positive PCR products and phylogenetic analysis for subtyping of the isolates. Overall, Blastocystis sp. was identified in 37.6% of the samples, with significant differences in frequency between animal groups (sheep, 65.5%; camels, 62.2%; goats, 36.0%; rabbits, 10.1%; horses, 3.3%). Mixed infections were reported in 35.7% of the Blastocystis sp.-positive samples. A wide range of subtypes (STs) with varying frequency were identified from single infections in ruminants including sheep (ST1-ST3, ST5, ST10, ST14, ST21, ST24, ST26, and ST40), goats (ST1, ST3, ST5, ST10, ST26, ST40, ST43, and ST44), and camels (ST3, ST10, ST21, ST24-ST26, ST30, and ST44). Most of them overlapped across these animal groups, highlighting their adaptation to ruminant hosts. In other herbivores, only three and two STs were evidenced in rabbits (ST1-ST3) and horses (ST3 and ST44), respectively. The greater occurrence and wider genetic diversity of parasite isolates among ruminants, in contrast to other herbivores, strongly suggested that dietary habits likely played a significant role in influencing both the colonization rates of Blastocystis sp. and ST preference. Of all the isolates subtyped herein, 66.3% were reported as potentially zoonotic, emphasizing the significant role these animal groups may play in transmitting the parasite to humans. These findings also expand our knowledge on the prevalence, genetic diversity, host specificity, and zoonotic potential of Blastocystis sp. in herbivores.

Chronic urticaria associated with Blastocystis hominis infection

Urticaria is a skin rash with several etiologic factors, including infectious agents. Blastocystis hominis is an intestinal protozoan parasite that has been linked to urticaria and skin lesions. The aim of this work was to investigate the association between B. hominis infection and chronic urticaria. In a case-control study, stool samples were obtained from 94 patients with chronic urticaria as case group and 285 healthy individuals as control group. Urticaria activity score 7 (UAS7) was used to score the severity of urticaria, classified as mild, moderate and intense. All stool samples underwent routine stool examinations, as well as polymerase chain reaction (PCR) for the detection of B. hominis. Molecular detection was carried out using the small subunit ribosomal RNA (SSU-rRNA) gene and the parasite subtypes were determined by sequencing. The rate of B. hominis infection was 21.3% (20 out of 94) and 17.2% (49 out of 285) between the case and control groups, respectively (p = 0.463). Three subtypes of B. hominis, including ST-1, ST-2 and ST-3, were detected in the case and control groups (ST-1 = 30% vs. 8.3%, ST-2 = 40% vs. 25% and ST-3 = 30% vs. 66.6% in the case and control group, respectively), which was statistically significant (p = 0.00001). However, no statistical differences were found between the severity of the urticaria and the B. hominis subtypes (p = 0.533). This study revealed a higher prevalence (but not significant) of B. hominis infection among patients with urticaria than healthy individuals. However, the results did not find a significant association between the subtypes of B. hominis and the severity of urticaria.

Fecal microbiota transplantation: current challenges and future landscapes

SUMMARYGiven the importance of gut microbial homeostasis in maintaining health, there has been considerable interest in developing innovative therapeutic strategies for restoring gut microbiota. One such approach, fecal microbiota transplantation (FMT), is the main "whole gut microbiome replacement" strategy and has been integrated into clinical practice guidelines for treating recurrent Clostridioides difficile infection (rCDI). Furthermore, the potential application of FMT in other indications such as inflammatory bowel disease (IBD), metabolic syndrome, and solid tumor malignancies is an area of intense interest and active research. However, the complex and variable nature of FMT makes it challenging to address its precise functionality and to assess clinical efficacy and safety in different disease contexts. In this review, we outline clinical applications, efficacy, durability, and safety of FMT and provide a comprehensive assessment of its procedural and administration aspects. The clinical applications of FMT in children and cancer immunotherapy are also described. We focus on data from human studies in IBD in contrast with rCDI to delineate the putative mechanisms of this treatment in IBD as a model, including colonization resistance and functional restoration through bacterial engraftment, modulating effects of virome/phageome, gut metabolome and host interactions, and immunoregulatory actions of FMT. Furthermore, we comprehensively review omics technologies, metagenomic approaches, and bioinformatics pipelines to characterize complex microbial communities and discuss their limitations. FMT regulatory challenges, ethical considerations, and pharmacomicrobiomics are also highlighted to shed light on future development of tailored microbiome-based therapeutics.

Microbiota and IBD: Current knowledge and future perspectives

Inflammatory Bowel Disease (IBD) is a chronic relapsing-remitting disease with a remarkable increase in incidence worldwide and a substantial disease burden. Although the pathophysiology is not fully elucidated yet an aberrant immune reaction against the intestinal microbiota and the gut microbial dysbiosis have been identified to play a major role. The composition of gut microbiota in IBD patients is distinct from that of healthy individuals, with certain organisms predominating over others. Differences in the microbial dysbiosis have been also observed between Crohn Disease (CD) and Ulcerative Colitis (UC). A disruption of the microbiota's balance can lead to inflammation and intestinal damage. Microbiota composition in IBD can be affected both by endogenous (i.e., interaction with the immune system and intestinal epithelial cells) and exogenous (i.e., medications, surgery, diet) factors. The complex interplay between the gut microbiota and IBD is an area of great interest for understanding disease pathogenesis and developing new treatments. The purpose of this review is to summarize the latest evidence on the role of microbiota in IBD pathogenesis and to explore possible future areas of research.

A mitochondrial carrier transports glycolytic intermediates to link cytosolic and mitochondrial glycolysis in the human gut parasite Blastocystis

Stramenopiles form a clade of diverse eukaryotic organisms, including multicellular algae, the fish and plant pathogenic oomycetes, such as the potato blight Phytophthora, and the human intestinal protozoan Blastocystis. In most eukaryotes, glycolysis is a strictly cytosolic metabolic pathway that converts glucose to pyruvate, resulting in the production of NADH and ATP (Adenosine triphosphate). In contrast, stramenopiles have a branched glycolysis in which the enzymes of the pay-off phase are located in both the cytosol and the mitochondrial matrix. Here, we identify a mitochondrial carrier in Blastocystis that can transport glycolytic intermediates, such as dihydroxyacetone phosphate and glyceraldehyde-3-phosphate, across the mitochondrial inner membrane, linking the cytosolic and mitochondrial branches of glycolysis. Comparative analyses with the phylogenetically related human mitochondrial oxoglutarate carrier (SLC25A11) and dicarboxylate carrier (SLC25A10) show that the glycolytic intermediate carrier has lost its ability to transport the canonical substrates malate and oxoglutarate. Blastocystis lacks several key components of oxidative phosphorylation required for the generation of mitochondrial ATP, such as complexes III and IV, ATP synthase, and ADP/ATP carriers. The presence of the glycolytic pay-off phase in the mitochondrial matrix generates ATP, which powers energy-requiring processes, such as macromolecular synthesis, as well as NADH, used by mitochondrial complex I to generate a proton motive force to drive the import of proteins and molecules. Given its unique substrate specificity and central role in carbon and energy metabolism, the carrier for glycolytic intermediates identified here represents a specific drug and pesticide target against stramenopile pathogens, which are of great economic importance.

Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development

Despite substantial progress in cancer microbiome research, recognized confounders and advances in absolute microbiome quantification remain underused; this raises concerns regarding potential spurious associations. Here we study the fecal microbiota of 589 patients at different colorectal cancer (CRC) stages and compare observations with up to 15 published studies (4,439 patients and controls total). Using quantitative microbiome profiling based on 16S ribosomal RNA amplicon sequencing, combined with rigorous confounder control, we identified transit time, fecal calprotectin (intestinal inflammation) and body mass index as primary microbial covariates, superseding variance explained by CRC diagnostic groups. Well-established microbiome CRC targets, such as Fusobacterium nucleatum, did not significantly associate with CRC diagnostic groups (healthy, adenoma and carcinoma) when controlling for these covariates. In contrast, the associations of Anaerococcus vaginalis, Dialister pneumosintes, Parvimonas micra, Peptostreptococcus anaerobius, Porphyromonas asaccharolytica and Prevotella intermedia remained robust, highlighting their future target potential. Finally, control individuals (age 22-80 years, mean 57.7 years, standard deviation 11.3) meeting criteria for colonoscopy (for example, through a positive fecal immunochemical test) but without colonic lesions are enriched for the dysbiotic Bacteroides2 enterotype, emphasizing uncertainties in defining healthy controls in cancer microbiome research. Together, these results indicate the importance of quantitative microbiome profiling and covariate control for biomarker identification in CRC microbiome studies.

Comparative molecular epidemiology, subtype distribution, and zoonotic potential of Blastocystis sp. in Equus animals (horses, donkeys, and mules) in northwestern Iran

A total of 500 fecal samples were collected from Equus animals in six different cities (Ardabil, Namin, Nir, Meshginshahr, Germi, and Khalkhal) of Ardabil Province, northwestern Iran, with 200 samples from horses, 200 from donkeys, and 100 from mules. Of the horse samples, 100 were from racing horses under special monitoring and care, while the remaining 100 were from non-racing horses, including those used for herding or in rural areas. All fecal samples were examined for the presence of Blastocystis sp. using PCR amplification of the SSU rRNA gene's barcode region after DNA extraction. The molecular prevalence of Blastocystis infection in Equus animals was 7.6% (38/500). Blastocystis was more common in horses [11.5% (23/200)] than in donkeys [5.5% (11/200)] and mules [4% (4/100)] (P > 0.05). Compared to racing horses [3% (3/100)], non-racing/rural horses [20% (20/100)] exhibited a substantially higher prevalence of Blastocystis (P < 0.05). The prevalence of Blastocystis in diarrheal samples and younger animals was remarkably higher than in formed samples and older animals, respectively (P < 0.05). No significant difference in Blastocystis infection prevalence was found between the genders of examined animals (P > 0.05). In Equus animals, 38 Blastocystis isolates included eight STs: ST10 [31.6% (12/38)], ST1 [21.1% (8/38)], ST2 [15.8% (6/38)], ST3 [10.5% (4/38)], ST4 [7.9% (3/38)], ST7 [5.2% (2/38)], ST14 [5.2% (2/38)], and ST6 [2.6% (1/38)]. These results suggest that Equus animals act as a proper reservoir for numerous Blastocystis STs, consequently playing a crucial part in the spread of this protozoan infection to humans, animals, and water reservoirs.

Blastocystis: A Mysterious Member of the Gut Microbiome

Blastocystis is the most common gastrointestinal protist found in humans and animals. Although the clinical significance of Blastocystis remains unclear, the organism is increasingly being viewed as a commensal member of the gut microbiome. However, its impact on the microbiome is still being debated. It is unclear whether Blastocystis promotes a healthy gut and microbiome directly or whether it is more likely to colonize and persist in a healthy gut environment. In healthy people, Blastocystis is frequently associated with increased bacterial diversity and significant differences in the gut microbiome. Based on current knowledge, it is not possible to determine whether differences in the gut microbiome are the cause or result of Blastocystis colonization. Although it is possible that some aspects of this eukaryote's role in the intestinal microbiome remain unknown and that its effects vary, possibly due to subtype and intra-subtype variations and immune modulation, more research is needed to characterize these mechanisms in greater detail. This review covers recent findings on the effects of Blastocystis in the gut microbiome and immune modulation, its impact on the microbiome in autoimmune diseases, whether Blastocystis has a role like bacteria in the gut-brain axis, and its relationship with probiotics.

Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing

Building models is essential for understanding the functions and dynamics of microbial communities. Metabolic models built on genome-scale metabolic network reconstructions (GENREs) are especially relevant as a means to decipher the complex interactions occurring among species. Model reconstruction increasingly relies on metagenomics, which permits direct characterisation of naturally occurring communities that may contain organisms that cannot be isolated or cultured. In this review, we provide an overview of the field of metabolic modelling and its increasing reliance on and synergy with metagenomics and bioinformatics. We survey the means of assigning functions and reconstructing metabolic networks from (meta-)genomes, and present the variety and mathematical fundamentals of metabolic models that foster the understanding of microbial dynamics. We emphasise the characterisation of interactions and the scaling of model construction to large communities, two important bottlenecks in the applicability of these models. We give an overview of the current state of the art in metagenome sequencing and bioinformatics analysis, focusing on the reconstruction of genomes in microbial communities. Metagenomics benefits tremendously from third-generation sequencing, and we discuss the opportunities of long-read sequencing, strain-level characterisation and eukaryotic metagenomics. We aim at providing algorithmic and mathematical support, together with tool and application resources, that permit bridging the gap between metagenomics and metabolic modelling.

Blastocystis: view from atop the gut-brain iceberg

Blastocystis is a common intestinal parasite that has been linked to gut pathology in humans. In this article, we highlight recent publications that offer insight into how these organisms can influence human cognition and the gut microbiome. We also suggest a potential mechanism of action by which this might occur.

Prevalence of Blastocystis sp. in Morocco: Comparative assessment of three diagnostic methods and characterization of parasite forms in Jones' culture medium

Blastocystosis is an infection caused by Blastocystis sp., which colonizes the digestive tract of various hosts, including humans, although its pathogenicity is debated. It is crucial to detect and distinguish the different forms of Blastocystis to understand better its impact on human health and its epidemiological evolution. This study evaluated three diagnostic methods on 105 stool samples: direct examination, culture in Jones' medium, and conventional PCR. PCR is considered the gold standard and revealed a high prevalence of Blastocystis (67.62%) compared to direct examination (20.95%) and culture in Jones' medium (51.43%). Although the sensitivity of direct examination and culture was 31% and 76.1%, respectively, their specificity was 100%. No significant risk factors were identified. A statistically significant association was observed between Blastocystis infection and abdominal pain. Microscopic analysis revealed various morphological forms. Molecular diagnosis is an essential tool to determine the true prevalence of Blastocystis, and studying the different forms of this microorganism will contribute to a better understanding of its biological cycle and, therefore, the impact of this emerging infection on human health.

Triangulating nutrigenomics, metabolomics and microbiomics toward personalized nutrition and healthy living

The unique physiological and genetic characteristics of individuals influence their reactions to different dietary constituents and nutrients. This notion is the foundation of personalized nutrition. The field of nutrigenetics has witnessed significant progress in understanding the impact of genetic variants on macronutrient and micronutrient levels and the individual's responsiveness to dietary intake. These variants hold significant value in facilitating the development of personalized nutritional interventions, thereby enabling the effective translation from conventional dietary guidelines to genome-guided nutrition. Nevertheless, certain obstacles could impede the extensive implementation of individualized nutrition, which is still in its infancy, such as the polygenic nature of nutrition-related pathologies. Consequently, many disorders are susceptible to the collective influence of multiple genes and environmental interplay, wherein each gene exerts a moderate to modest effect. Furthermore, it is widely accepted that diseases emerge because of the intricate interplay between genetic predisposition and external environmental influences. In the context of this specific paradigm, the utilization of advanced "omic" technologies, including epigenomics, transcriptomics, proteomics, metabolomics, and microbiome analysis, in conjunction with comprehensive phenotyping, has the potential to unveil hitherto undisclosed hereditary elements and interactions between genes and the environment. This review aims to provide up-to-date information regarding the fundamentals of personalized nutrition, specifically emphasizing the complex triangulation interplay among microbiota, dietary metabolites, and genes. Furthermore, it highlights the intestinal microbiota's unique makeup, its influence on nutrigenomics, and the tailoring of dietary suggestions. Finally, this article provides an overview of genotyping versus microbiomics, focusing on investigating the potential applications of this knowledge in the context of tailored dietary plans that aim to improve human well-being and overall health.

Effects of Lactiplantibacillus plantarum and Lacticaseibacillus paracasei supplementation on the single-cell fecal parasitome in children with celiac disease autoimmunity: a randomized, double-blind placebo-controlled clinical trial

BACKGROUND

Lactiplantibacillus plantarum HEAL9 and Lacticaseibacillus paracasei 8700:2 positively affect the fecal bacteriome in children with celiac disease autoimmunity after 6 months of supplementation. The aim of the present investigation was to study the effects of Lactiplantibacillus plantarum HEAL9 and Lacticaseibacillus paracasei 8700:2 on the single-cell parasitome, with a primary focus on Blastocystis.

METHODS

Stool samples were collected from 78 Swedish children with celiac disease autoimmunity participating in a randomized, double-blind, placebo-controlled clinical trial to either receive a mixture of supplementation with L. plantarum HEAL9 and L. paracasei 8700:2 (n = 38) or placebo (n = 40). A total of 227 stool samples collected at baseline and after 3 and 6 months of intervention, respectively, were retrospectively analyzed for Blastocystis by quantitative real-time PCR and subtyped by massively parallel amplicon sequencing. Other single-cell parasites were detected by untargeted 18S rDNA amplicon sequencing and verified by real-time PCR. The relation between the parasites and the bacteriome community was characterized by using 16S rDNA profiling of the V3-V4 region.

RESULTS

Three different single-cell protists were identified, of which the highest prevalence was found for Dientamoeba fragilis (23.1%, 18/78 children), followed by Blastocystis (15.4%, 12/78) and Entamoeba spp. (2.6%, 2/78). The quantity of the protists was stable over time and not affected by probiotic intervention (P = 0.14 for Blastocystis, P = 0.10 for D. fragilis). The positivity of the protists was associated with increased bacteriome diversity (measured by multiple indices, P < 0.03). Bacterial composition was influenced by the presence of the protists: positivity of Blastocystis was inversely associated with Akkermansia (at the levels of the genus as well as its family, order, class and phylum); P < 0.002), Faecalibacterium (P = 0.003) and Romboutsia (P = 0.029); positivity of D. fragilis was inversely associated with families Enterobacteriaceae (P = 0.016) and Coriobacteriaceae (P = 0.022) and genera Flavonifractor (P < 0.001), Faecalibacterium (P = 0.009), Lachnoclostridium (P = 0.029), Ruminococcus (P < 0.001) and Granulicatella (P = 0.018).

CONCLUSIONS

The prevalence of single-cell protists is low in children with celiac disease autoimmunity. The colonization was stable regardless of the probiotic intervention and associated with increased diversity of the fecal bacteriome but inversely associated with some beneficial bacteria.

Intraspecific microdiversity and ecological drivers of lactic acid bacteria in naturally fermented milk ecosystem

Traditional fermented milks are produced by inoculating technique, which selects well-adapted microorganisms that have been passed on through generations. Few reports have used naturally fermented milks as model ecosystems to investigate the mechanism of formation of intra-species microbial diversity. Here, we isolated and whole-genome-sequenced a total of 717 lactic acid bacterial isolates obtained from 12 independent naturally fermented milks collect from 12 regions across five countries. We further analyzed the within-sample intra-species phylogenies of 214 Lactobacillus helveticus isolates, 97 Lactococcus lactis subsp. lactis isolates, and 325 Lactobacillus delbrueckii subsp. bulgaricus isolates. We observed a high degree of intra-species genomic and functional gene diversity within-/between-sample(s). Single nucleotide polymorphism-based phylogenetic reconstruction revealed great within-sample intra-species heterogeneity, evolving from multiple lineages. Further phylogenetic reconstruction (presence-absence gene profile) revealed within-sample inter-clade functional diversity (based on carbohydrate-active enzyme- and peptidase-encoding genes) in all three investigated species/subspecies. By identifying and mapping clade-specific genes of intra-sample clades of the three species/subspecies to the respective fermented milk metagenome, we found extensive potential inter-/intra-species horizontal gene transfer events. Finally, the microbial composition of the samples is closely linked to the nucleotide diversity of the respective species/subspecies. Overall, our results contribute to the conservation of lactic acid bacteria resources, providing ecological insights into the microbial ecosystem of naturally fermented dairy products.

Identification and validation of novel Blastocystis subtype ST41 in a Colombian patient undergoing colorectal cancer screening

Blastocystis sp. is among the most frequent intestinal protists identified in humans globally. However, characterization of Blastocystis subtype diversity in humans is ongoing. We report here the identification of novel Blastocystis subtype ST41 in a Colombian patient undergoing colorectal cancer screening involving colonoscopy and fecal testing (microscopy, culture, PCR). The full-length ssu rRNA gene sequence of the protist was generated using MinION long-read sequencing technology. The validity of the novel subtype was confirmed via phylogenetic and pairwise distance analyses of the full-length ST41 sequence and all other valid subtypes. The study provides reference material essential for conducting subsequent experimental studies.

Metataxomics reveals Blastocystis subtypes mixed infections in Colombian children

Blastocystis sp., is an intestinal protist with a broad host range and a high prevalence in human populations worldwide, even in developed Western countries. The publication of conflicting evidence has divided the scientific community about the pathogenic role of this parasite. Even though, genetic studies on Blastocystis sp. revealed associations between genotypes and different pathogenic profiles. Conventionally, the detection of this parasite is based on microscopic or PCR methods, which offer meager or null performance in detecting mixed infections. In this work, we applied a metataxonomic NGS approach targeting the V4 region of the eukaryotic SSU-rRNA gene and classical phylogenetic methods. This approach allowed us to detect Blastocystis sp. in stool samples from infected children living in an urban setting in the city of Medellin attending the same daycare center. Phylogenetic analysis identified the subtypes present in the children as ST1, ST2, and ST3. Besides, mixed infections of subtypes ST1 + ST3 were spotted in 16% of the analyzed stool samples.

Differential gut microbiome in spondyloarthritis patients associated to Blastocystis colonization

The role of Blastocystis in intestinal health is an open controversy, and little is known about the potential effect of this microorganism in autoinflammatory diseases such as spondyloarthritis (SpA). Here, we analyzed the gut microbiome of 36 SpA patients and 13 control individuals and demonstrated that the richness, diversity, and taxonomic composition between these two groups are different. We also showed that colonization by Blastocystis in control individuals increases the richness and diversity of the intestinal microbiome, whereas in SpA patients, it does not seem to have any impact. This may reflect a potential role of Blastocystis in sculpting the gut microbiome architecture in control individuals, whereas in subjects with SpA, the modulation of the microbiome may be governed by disease-dependent factors that cannot be overcome by Blastocystis. Regarding taxonomic characterization, SpA patients colonized by Blastocystis showed significant increases in the phylum Pseudomonadota, class Gammaproteobacteria, family Succinivibrionaceae, and genus Succinivibrio. Simultaneously, there were significant increases in the class Bacilli, order Lactobacillales, families Lactobacillaceae and Clostridiaceae, and genera Lactobacillus and Clostridium in non-colonized SpA patients. On the other hand, PICRUSt analysis in Blastocystis-positive SpA patients showed elevations in pathways that may enhance antioxidant capacities and alleviate intestinal inflammation, while Blastocystis-negative SpA patients showed significant changes in pathways that promote cell division/proliferation and can lead to larger changes in the gut microbiome. Our analyses lead us to believe that these changes in the gut microbiome of SpA patients may trigger protective mechanisms as an initial response to inflammation in an attempt to restore balance in the intestinal environment.

Epidemiology of Blastocystis Infection: A Review of Data from Poland in Relation to Other Reports

Blastocystis is a common gut protist of humans and various animals worldwide, with a high level of genetic diversity. Neither its zoonotic potential and transmission routes nor its pathogenicity are fully known. This fact, and the fact that Blastocystis is the most abundant eukaryote in human faeces, raises the question of its relevance to public health. Here, we summarise (in relation to other reports) the results of studies on the prevalence and genotypic variation of Blastocystis, which were carried out in animals, humans, and in water environments in Poland. In humans, the prevalence ranged between 0.14 and 23.6%, in some animals reached 58.97%, and in water environments was 5.1%. Seven subtypes were identified in humans (ST1-ST4, ST6, ST7, and ST9), of which ST3 was the most common. Among animals (wild, livestock, and pet animals), eleven STs were identified, with differential host specificity. Humans and animals shared ST1, ST2, ST3, ST6, and ST7, while ST1 and ST3 were present in humans, animals, and water sources. These observations indicate the possibility of Blastocystis transmission between animals and humans. Further studies should be continued in search of the sources and transmission routes of Blastocystis in order to prevent the spread of infections among humans and animals.

The eukaryome of African children is influenced by geographic location, gut biogeography, and nutritional status

Eukaryotes have historically been studied as parasites, but recent evidence suggests they may be indicators of a healthy gut ecosystem. Here, we describe the eukaryome along the gastrointestinal tract of children aged 2-5 years and test for associations with clinical factors such as anaemia, intestinal inflammation, chronic undernutrition, and age. Children were enrolled from December 2016 to May 2018 in Bangui, Central African Republic and Antananarivo, Madagascar. We analyzed a total of 1104 samples representing 212 gastric, 187 duodenal, and 705 fecal samples using a metabarcoding approach targeting the full ITS2 region for fungi, and the V4 hypervariable region of the 18S rRNA gene for the overall eukaryome. Roughly, half of all fecal samples showed microeukaryotic reads. We find high intersubject variability, only a handful of taxa that are likely residents of the gastrointestinal tract, and frequent co-occurrence of eukaryotes within an individual. We also find that the eukaryome differs between the stomach, duodenum, and feces and is strongly influenced by country of origin. Our data show trends towards higher levels of Fusarium equiseti, a mycotoxin producing fungus, and lower levels of the protist Blastocystis in stunted children compared to nonstunted controls. Overall, the eukaryome is poorly correlated with clinical variables. Our study is of one of the largest cohorts analyzing the human intestinal eukaryome to date and the first to compare the eukaryome across different compartments of the gastrointestinal tract. Our results highlight the importance of studying populations across the world to uncover common features of the eukaryome in health.

Protozoan predation as a driver of diversity and virulence in bacterial biofilms

Protozoa are eukaryotic organisms that play a crucial role in nutrient cycling and maintaining balance in the food web. Predation, symbiosis and parasitism are three types of interactions between protozoa and bacteria. However, not all bacterial species are equally susceptible to protozoan predation as many are capable of defending against predation in numerous ways and may even establish either a symbiotic or parasitic life-style. Biofilm formation is one such mechanism by which bacteria can survive predation. Structural and chemical components of biofilms enhance resistance to predation compared to their planktonic counterparts. Predation on biofilms gives rise to phenotypic and genetic heterogeneity in prey that leads to trade-offs in virulence in other eukaryotes. Recent advances, using molecular and genomics techniques, allow us to generate new information about the interactions of protozoa and biofilms of prey bacteria. This review presents the current state of the field on impacts of protozoan predation on biofilms. We provide an overview of newly gathered insights into (i) molecular mechanisms of predation resistance in biofilms, (ii) phenotypic and genetic diversification of prey bacteria, and (iii) evolution of virulence as a consequence of protozoan predation on biofilms.

Investigating causal associations among gut microbiota, metabolites, and liver diseases: a Mendelian randomization study

Objective

There is some evidence for an association between gut microbiota and nonalcoholic fatty liver disease (NAFLD), alcoholic liver disease (ALD), and viral hepatitis, but no studies have explored their causal relationship.

Methods

Instrumental variables of the gut microbiota (N = 13266) and gut microbiota-derived metabolites (N = 7824) were acquired, and a Mendelian randomization study was performed to explore their influence on NAFLD (1483 European cases and 17,781 European controls), ALD (2513 European cases and 332,951 European controls), and viral hepatitis risk (1971 European cases and 340,528 European controls). The main method for examining causality is inverse variance weighting (IVW).

Results

IVW results confirmed that Anaerotruncus (p = 0.0249), Intestinimonas (p = 0.0237), Lachnoclostridium (p = 0.0245), Lachnospiraceae NC2004 group (p = 0.0083), Olsenella (p = 0.0163), and Peptococcus (p = 0.0472) were protective factors for NAFLD, and Ruminococcus 1 (p = 0.0120) was detrimental for NAFLD. The higher abundance of three genera, Lachnospira (p = 0.0388), Desulfovibrio (p = 0.0252), and Ruminococcus torques group (p = 0.0364), was correlated with a lower risk of ALD, while Ruminococcaceae UCG 002 level was associated with a higher risk of ALD (p = 0.0371). The Alistipes (p = 0.0069) and Ruminococcaceae NK4A214 group (p = 0.0195) were related to a higher risk of viral hepatitis. Besides, alanine (p = 0.0076) and phenyllactate (p = 0.0100) were found to be negatively correlated with NAFLD, while stachydrine (Op = 0.0244) was found to be positively associated with NAFLD. The phenylacetate (p = 0.0353) and ursodeoxycholate (p = 0.0144) had a protective effect on ALD, while the threonate (p = 0.0370) exerted a detrimental influence on ALD. The IVW estimates of alanine (p = 0.0408) and cholate (p = 0.0293) showed their suggestive harmful effects against viral hepatitis, while threonate (p = 0.0401) displayed its suggestive protective effect against viral hepatitis.

Conclusion

In conclusion, our research supported causal links between the gut microbiome and its metabolites and NAFLD, ALD, and viral hepatitis.

Talk to Me-Interplay between Mitochondria and Microbiota in Aging

The existence of mitochondria in eukaryotic host cells as a remnant of former microbial organisms has been widely accepted, as has their fundamental role in several diseases and physiological aging. In recent years, it has become clear that the health, aging, and life span of multicellular hosts are also highly dependent on the still-residing microbiota, e.g., those within the intestinal system. Due to the common evolutionary origin of mitochondria and these microbial commensals, it is intriguing to investigate if there might be a crosstalk based on preserved common properties. In the light of rising knowledge on the gut-brain axis, such crosstalk might severely affect brain homeostasis in aging, as neuronal tissue has a high energy demand and low tolerance for according functional decline. In this review, we summarize what is known about the impact of both mitochondria and the microbiome on the host's aging process and what is known about the aging of both entities. For a long time, bacteria were assumed to be immortal; however, recent evidence indicates their aging and similar observations have been made for mitochondria. Finally, we present pathways by which mitochondria are affected by microbiota and give information about therapeutic anti-aging approaches that are based on current knowledge.

Blastocystis sp. reduces the efficacy of 5-fluorouracil as a colorectal cancer chemotherapeutic treatment

Blastocystis is an enteric protozoan parasite with extensive genetic variation and unclear pathogenicity. It is commonly associated with gastrointestinal symptoms such as nausea, diarrhea, vomiting and abdominal pain in immunocompromised individuals. In this study, we explored the in vitro and in vivo effects of Blastocystis on the activity of a commonly used CRC chemotherapeutic agent, 5-FU. The cellular and molecular effects of solubilized antigen of Blastocystis in the presence of 5-FU were investigated using HCT116, human CRC cell line and CCD 18-Co, normal human colon fibroblast cells. For the in vivo study, 30 male Wistar rats were divided into six groups, as follows; Control Group: oral administration of 0.3ml Jones' medium, Group A: rats injected with azoxymethane (AOM), Group A-30FU: Rats injected with AOM and administered 30mg/kg 5-FU, Group B-A-30FU: rats inoculated with Blastocystis cysts, injected with AOM and administered 30mg/kg 5-FU, Group A-60FU: rats injected with AOM and administered 60mg/kg 5-FU and Group B-A-60FU: rats inoculated with Blastocystis cysts, injected with AOM and administered 60mg/kg 5-FU. The in vitro study revealed that the inhibitory potency of 5-FU at 8μM and 10μM was reduced from 57.7% to 31.6% (p < 0.001) and 69.0%-36.7% (p < 0.001) respectively when co-incubated with Blastocystis antigen for 24 h. However, the inhibitory potency of 5-FU in CCD-18Co cells was not significantly affected in the presence of Blastocystis antigen. The reduced inhibitory potency of 5-FU against cancer cell proliferation due to the presence of Blastocystis is consistent with the upregulation of expression of type 2 cytokines, transforming growth factor (TGF-β) and nuclear factor E2-related factor 2 (Nrf2) gene expression. Increased inflammation and abnormal histopathological findings along with a significant cancer multiplicity and adenoma incidence were evident in the intestine of the B-A-30FU and B-A-60FU groups when compared with the A-30FU and A-60FU groups respectively. Our in vitro and in vivo findings indicate that Blastocystis infection could potentially interfere with chemotherapy regimens such as 5-FU in CRC patients undergoing chemotherapy.

Molecular identification and genotyping of Blastocystis sp. in sheep and goats from some areas in Inner Mongolia, Northern China

Blastocystis sp. is a kind of unicellular intestinal commensal which is widely distributed in humans and animals, and frequently found in the people who are in close contact with animals. To investigate the prevalence and evaluate the zoonotic potential of Blastocystis sp. in sheep and goats from Inner Mongolia, China, a total of 1037 samples were collected from them, and subjected to nested PCR amplification based on the small subunit ribosomal RNA (SSU rRNA) gene of Blastocystis sp. The sanger sequencing was used for Blastocystis sp. subtype identification. The results indicated that the average infection rate of Blastocystis sp. was 10.70% [95CI: 8.82%-12.58%] (111/1037), including 11.30% [95CI: 7.96%-14.64%] for sheep (39/345) and 10.40% [95CI: 8.13%-12.67%] for goats (72/692). Five Blastocystis subtypes (ST5, ST10, ST14, ST21 and ST26) were identified in the present study. Among them, ST10 was the most dominant subtype in sheep and goats, accounting for 70.27% (78/111) of the total identified positive samples. This is the first report regarding Blastocystis sp. subtypes ST21 and ST26 in goats in China. This study has provided a detail epidemiological data on the prevalence and subtypes distribution of Blastocystis sp. in sheep and goats in Inner Mongolia, China. Our results indicated that sheep and goats could be reservoir host for multiple Bastocystis subtypes, including the zoonotic subtypes. Further studies among humans, livestock and wild animals are needed to better understand their role in the spread of Blastocystis sp.

Circulation and colonisation of Blastocystis subtypes in schoolchildren of various ethnicities in rural northern Thailand

Blastocystis is a protist of controversial pathogenicity inhabiting the gut of humans and other animals. Despite a century of intense study, understanding of the epidemiology of Blastocystis remains fragmentary. Here, we aimed to explore its prevalence, stability of colonisation and association with various factors in a rural elementary school in northern Thailand. One hundred and forty faecal samples were collected from 104 children at two time points (tp) 105 days apart. For tp2, samples were also obtained from 15 animals residing on campus and seven water locations. Prevalence in children was 67% at tp1 and 89% at tp2, 63% in chickens, 86% in pigs, and 57% in water. Ten STs were identified, two of which were shared between humans and animals, one between animals and water, and three between humans and water. Eighteen children (out of 36) carried the same ST over both time points, indicating stable colonisation. Presence of Blastocystis (or ST) was not associated with body mass index, ethnicity, birth delivery mode, or milk source as an infant. This study advances understanding of Blastocystis prevalence in an understudied age group, the role of the environment in transmission, and the ability of specific STs to stably colonise children.

Colonization with ubiquitous protist Blastocystis ST1 ameliorates DSS-induced colitis and promotes beneficial microbiota and immune outcomes

Blastocystis is a species complex that exhibits extensive genetic diversity, evidenced by its classification into several genetically distinct subtypes (ST). Although several studies have shown the relationships between a specific subtype and gut microbiota, there is no study to show the effect of the ubiquitous Blastocystis ST1 on the gut microbiota and host health. Here, we show that Blastocystis ST1 colonization increased the proportion of beneficial bacteria Alloprevotella and Akkermansia, and induced Th2 and Treg cell responses in normal healthy mice. ST1-colonized mice showed decreases in the severity of DSS-induced colitis when compared to non-colonized mice. Furthermore, mice transplanted with ST1-altered gut microbiota were refractory to dextran sulfate sodium (DSS)-induced colitis via induction of Treg cells and elevated short-chain fat acid (SCFA) production. Our results suggest that colonization with Blastocystis ST1, one of the most common subtypes in humans, exerts beneficial effects on host health through modulating the gut microbiota and adaptive immune responses.

Molecular epidemiology and subtyping of Blastocystis sp. and its subtypes in celiac patients; a case control study

Blastocystis sp. is a common intestinal protist, reported from symptomatic and asymptomatic subjects. Blastocystis sp. has been reported from a broad spectrum of gastrointestinal disorders. Celiac disease (CD) is an autoimmune disorder of the small intestine, which leads to the lack of tolerance against gluten. Long-term following of gluten-free diet in CD patients decreases the gut microbiota restoration and probably decreases the chance of Blastocystis sp. colonization. The current study aimed to investigate the prevalence of Blastocystis sp. and its subtypes in CD patients in comparison to healthy subjects. Stool samples were collected from 238 participants including 92 confirmed CD patients and 146 healthy subjects. upon DNA extraction, the presence of Blastocystis sp. was evaluated using amplification of discriminative regions of the small ribosomal RNA (ssu rRNA) gene. To characterize subtypes and alleles, amplified fragments were sequenced. Phylogenetic trees were constructed to visualize subtype correlation. Our findings showed that 21% (50) of samples including 16.3% (15/92) and 23.97% (35/146) were positive for Blastocystis sp. in CD patients and healthy controls, respectively. Except family relationship, other variables were not statistical correlated with the presence of Blastocystis sp.. Totally, 25 samples were successfully sequenced. Accordingly, ST1, ST2, and ST3 were present in 8 (32%), 9 (36%), and 8 (32%) of the samples, respectively. Allele discrimination showed that all ST1 were allele 4; alleles 11, 9, and 12 were retrieved from ST2, and alleles 34, 36, and 38 were observed in ST3. The relationship between colonization of Blastocystis sp. and alteration in the gut microbiota composition is indeterminate, however, this hypothesis that lower prevalence of Blastocystis sp. in CD patients who follow a gluten-free diet affect the colonization of Blastocystis sp. via alteration in the gut microbiota composition could be interesting for further investigations.

First Epidemiological Survey on the Prevalence and Subtypes Distribution of the Enteric Parasite Blastocystis sp. in Vietnam

Although Blastocystis sp. is the most common enteric protozoan in human stools worldwide, various geographical areas remain to be investigated regarding the frequency and circulation of this parasite. Such is the case of some developing countries in Southeast Asia that exhibit a higher risk for parasitic infections due to unsanitary conditions. While several epidemiological surveys have been conducted, for instance, in Thailand, little or no data are available from neighboring countries, such as Vietnam. Therefore, in order to determine the prevalence and subtype (ST) distribution of Blastocystis sp. and to clarify the transmission of the parasite, the first molecular epidemiological survey ever conducted in this country was performed. For this purpose, a total of 310 stool specimens were collected from patients enrolled at the Family Hospital of Da Nang and then tested for the presence of Blastocystis sp. by real-time Polymerase Chain Reaction (qPCR), followed by subtyping of the isolates. The overall prevalence of the parasite reached 34.5% in this Vietnamese cohort. No significant association was found between parasite infection and gender, age, symptomatic status, contact with animals or source of drinking water. Out of the 107 positive patients, nearly half presented mixed infections. Therefore, some of the corresponding samples were reanalyzed by end-point PCR, followed by PCR products cloning and sequencing. Of the 88 total subtyped isolates, ST3 was predominant, followed by ST10, ST14, ST7, ST1, ST4, ST6 and ST8. Our study was, thus, the first to report ST8, ST10 and ST14 in the Southeast Asian population. The predominance of ST3 within this Vietnamese cohort, coupled with its low intra-ST genetic variability, reflected a large inter-human transmission, while ST1 transmission was suggested to be not only anthroponotic, but also likely correlated to animal or environmental sources. Strikingly, isolates considered of animal origin (ST6-ST8, ST10 and ST14) accounted for more than 50% of the subtyped isolates. These findings improved our knowledge of the epidemiology and circulation of Blastocystis sp. in Southeast Asia, and in particular, in Vietnam, and highlighted both a major burden of the parasite in this country and a high risk of zoonotic transmission, mainly from poultry and livestock.

Gut bacteria influence Blastocystis sp. phenotypes and may trigger pathogenicity

Whilst the influence of intestinal microbiota has been shown in many diseases such as irritable bowel syndrome, colorectal cancer, and aging, investigations are still scarce on its role in altering the nature of other infective organisms. Here we studied the association and interaction of Blastocystis sp. and human intestinal microbiota. In this study, we investigated the gut microbiome of Blastocystis sp.-free and Blastocystis sp. ST3-infected individuals who are symptomatic and asymptomatic. We tested if the expression of phenotype and pathogenic characteristics of Blastocystis sp. ST3 was influenced by the alteration of its accompanying microbiota. Blastocystis sp. ST3 infection alters bacterial composition. Its presence in asymptomatic individuals showed a significant effect on microbial richness compared to symptomatic ones. Inferred metagenomic findings suggest that colonization of Blastocystis sp. ST3 could contribute to the alteration of microbial functions. For the first time, we demonstrate the influence of bacteria on Blastocystis sp. pathogenicity. When Blastocystis sp. isolated from a symptomatic individual was co-cultured with bacterial suspension of Blastocystis sp. from an asymptomatic individual, the parasite demonstrated increased growth and reduced potential pathogenic expressions. This study also reveals that Blastocystis sp. infection could influence microbial functions without much effect on the microbiota diversity itself. Our results also demonstrate evidence on the influential role of gut microbiota in altering the characteristics of the parasite, which becomes the basis for the contradictory findings on the parasite's pathogenic role seen across different studies. Our study provides evidence that asymptomatic Blastocystis sp. in a human gut can be triggered to show pathogenic characteristics when influenced by the intestinal microbiota.