Contrasting Strategies: Human Eukaryotic Versus Bacterial Microbiome Research

Hooks, Katarzyna B.; O’Malley, Maureen A.

doi:10.1111/jeu.12766

Cited by 23 publications

(16 citation statements)

References 171 publications

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“…The gut microbiome harbors thousands of species of archaea, bacteria, viruses and eukaryotes such as protists and fungi that contribute to host biology. The gut eukaryotic communities of monogastric species show a higher interindividual variability, but less abundance, diversity and richness than their bacterial counterparts [1]. The so called gut mycobiome of healthy humans is dominated by fungal genera like Saccharomyces, Candida, Penicillim, Aspergillus and Malassezia [2], while protist genera such as Blastocystis, Entamoeba and Enteromonas have been reported in the human gut across different geographical location [3][4][5].…”

Section: Introductionmentioning

confidence: 99%

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Gut eukaryotic communities in pigs: diversity, composition and host genetics contribution

et al. 2020

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Background: The pig gut microbiome harbors thousands of species of archaea, bacteria, viruses and eukaryotes such as protists and fungi. However, since the majority of published studies have been focused on prokaryotes, little is known about the diversity, host-genetic control, and contributions to host performance of the gut eukaryotic counterparts. Here we report the first study that aims at characterizing the diversity and composition of gut commensal eukaryotes in pigs, exploring their putative control by host genetics, and analyzing their association with piglets body weight. Results: Fungi and protists from the faeces of 514 healthy Duroc pigs of two sexes and two different ages were characterized by 18S and ITS ribosomal RNA gene sequencing. The pig gut mycobiota was dominated by yeasts, with a high prevalence and abundance of Kazachstania spp. Regarding protists, representatives of four genera (Blastocystis, Neobalantidium, Tetratrichomonas and Trichomitus) were predominant in more than the 80% of the pigs. Heritabilities for the diversity and abundance of gut eukaryotic communities were estimated with the subset of 60d aged piglets (N = 390). The heritabilities of α-diversity and of the abundance of fungal and protists genera were low, ranging from 0.15 to 0.28. A genome wide association study reported genetic variants related to the fungal α-diversity and to the abundance of Blastocystis spp. Annotated candidate genes were mainly associated with immunity, gut homeostasis and metabolic processes. Additionally, we explored the association of gut commensal eukaryotes with piglet body weight. Our results pointed to a positive contribution of fungi from the Kazachstania genus, while protists displayed both positive (Blastocystis and Entamoeba) and negative (Trichomitus) associations with piglet body weight. Conclusions: Our results point towards a minor and taxa specific genetic control over the diversity and composition of the pig gut eukaryotic communities. Moreover, we provide evidences of the associations between piglets' body weight after weaning and members from the gut fungal and protist eukaryote community. Overall, this study highlights the relevance of considering, along with that of bacteria, the contribution of the gut eukaryote communities to better understand host-microbiome association and their role on pig performance, welfare and health.

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Section: Introductionmentioning

confidence: 99%

“…CK8166 and (c) Fungi Alpha diversity. The x-axis represents the pig autosomal chromosomes(1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18), and the y-axis the significance level represented as the -log 10 (P-value)…”

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confidence: 99%

Gut eukaryotic communities in pigs: diversity, composition and host genetics contribution

et al. 2020

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“…Dysbiosis can be defined as changes in the communities of the microbiota that lead to a state of disease [13,14]. For instance, dysbiosis may be a common scenario in cases of diarrhea associated with the extensive use of antibiotics, which in turn allows C. difficile infection in the intestine [15].…”

Section: Introductionmentioning

confidence: 99%

Occurrence of Blastocystis in Patients with Clostridioides difficile Infection

et al. 2020

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Clostridiodes difficile comprises a public-health threat that has been understudied in Colombia. Hypervirulent strains of C. difficile harbor multiple toxins, can be easily spread, and can have their onset of disease within healthcare facilities (HCFO) and the community (CO). Studies have shown that a disrupted microbiota (e.g., dysbiosis) may allow C. difficile infection (CDI). It has been suggested that dysbiosis prevents colonization by the anaerobic eukaryote Blastocystis, possibly due to an increase in luminal oxygen tension. No study has found co-occurrence of CDI and Blastocystis. Therefore, we aimed to determine the frequencies of C. difficile and Blastocystis infection/colonization in 220 diarrheal fecal samples. Molecular detection by PCR for both microorganisms was performed, with descriptive analyses of four variables (CDI detection, determination of C. difficile toxigenic profiles, Blastocystis detection, and patient site of onset). We demonstrate a significant association between the presence of Blastocystis and CDI, with coinfection found in 61 patients, and show a high frequency of CDI among both HCFO and CO groups. Our results of coinfection frequencies could support hypotheses that suggest Blastocystis can adapt to dysbiosis and oxidative stress. Further, the presence of toxigenic C. difficile occurring outside healthcare facilities shown here raises the alarm for community wide spread.

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“…However, emerging evidence points toward critical roles in multiple other organs and tissues, which warrants substantial additional research. Although crucial insights have been gained into activation of innate immune sensors in response to bacterial motifs, eukaryotic activation originating from fungi and protozoa, which not only account for important pathogens but constitute an integral and important part of the host's microbiome, 218 is largely unexplored. The same limitations apply to the host's virome, which accounts for the most abundant and fastest mutating genetic elements on Earth 219 .…”

Section: Challenges and Limitationsmentioning

confidence: 99%

The microbiome and cytosolic innate immune receptors

Liwinski

Zheng

Elinav

2020

Immunological Reviews

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The discovery of innate immune sensors (pattern recognition receptors, PRRs) has profoundly transformed the notion of innate immunity, in providing a mechanistic basis for host immune interactions with a wealth of environmental signals, leading to a variety of immune‐mediated outcomes including instruction and activation of the adaptive immune arm. As part of this growing understanding of host‐environmental cross talk, an intimate connection has been unveiled between innate immune sensors and signals perceived from the commensal microbiota, which may be regarded as a hub integrating a variety of environmental cues. Among cytosolic PRRs impacting on host homeostasis by interacting with the commensal microbiota are nucleotide‐binding domain, leucine‐rich repeat‐containing protein receptors (NLRs), together with a number of cytosolic DNA sensors and the family of absent in melanoma (AIM)–like receptors (ALRs). NLR sensors have been a particular focus of research, and some NLRs have emerged as key orchestrators of inflammatory responses and host homeostasis. Some NLRs achieve this through the formation of cytoplasmic multiprotein complexes termed inflammasomes. More recently discovered PRRs include retinoic acid‐inducible gene‐I (RIG‐I)–like receptors (RLRs), cyclic GMP‐AMP synthase (cGAS), and STING. In the present review, they summarize recent advancements in knowledge on structure and function of cytosolic PRRs and their roles in host‐microbiota cross talk and immune surveillance. In addition, we discuss their relevance for human health and disease and future therapeutic applications involving modulation of their activation and signaling.

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Contrasting Strategies: Human Eukaryotic Versus Bacterial Microbiome Research

Cited by 23 publications

References 171 publications

Gut eukaryotic communities in pigs: diversity, composition and host genetics contribution

Gut eukaryotic communities in pigs: diversity, composition and host genetics contribution

Occurrence of Blastocystis in Patients with Clostridioides difficile Infection

The microbiome and cytosolic innate immune receptors

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