Intestinal fungi are causally implicated in microbiome assembly and immune development in mice

Bernardes, Erik van Tilburg; Pettersen, Veronika Kuchařová; Gutierrez, Mackenzie W.; Laforest‐Lapointe, Isabelle; Jendzjowsky, Nicholas G.; Cavin, Jean‐Baptiste; Vicentini, Fernando; Keenan, Catherine M.; Ramay, Hena R.; Samara, Jumana; MacNaughton, Wallace K.; Wilson, Richard J. A.; Kelly, Margaret M.; McCoy, Kathy D.; Sharkey, Keith A.; Arrieta, Marie‐Claire

doi:10.1038/s41467-020-16431-1

Cited by 165 publications

(117 citation statements)

References 67 publications

Supporting

Mentioning

113

Contrasting

Unclassified

Order By: Relevance

“…We deliberately focused on bacteria, which are dominant members of the ecosystem. This is not a sign of neglecting other microbes and viruses in the pig intestine [88][89][90][91][92] , but rather that the diversity of microbes to be catalogued is tremendous and that the required cultivation efforts are colossal if not tailored. As in recently published studies [93][94][95] , in order to capture as much diversity as possible, we employed an array of rich and selective culture media (see listing and composition in the previous section) in combination with samples from different gut locations (albeit mostly faeces) and pigs of various origins (most of the pigs were from one animal facility in Germany; others originated from two facilities in the USA or were wild boars from a farm in Canada; see detailed listing in Supplementary Data 1).…”

Section: Methodsmentioning

confidence: 99%

A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity

et al. 2020

View full text Add to dashboard Cite

Our knowledge about the gut microbiota of pigs is still scarce, despite the importance of these animals for biomedical research and agriculture. Here, we present a collection of cultured bacteria from the pig gut, including 110 species across 40 families and nine phyla. We provide taxonomic descriptions for 22 novel species and 16 genera. Meta-analysis of 16S rRNA amplicon sequence data and metagenome-assembled genomes reveal prevalent and pig-specific species within Lactobacillus, Streptococcus, Clostridium, Desulfovibrio, Enterococcus, Fusobacterium, and several new genera described in this study. Potentially interesting functions discovered in these organisms include a fucosyltransferase encoded in the genome of the novel species Clostridium porci, and prevalent gene clusters for biosynthesis of sactipeptide-like peptides. Many strains deconjugate primary bile acids in in vitro assays, and a Clostridium scindens strain produces secondary bile acids via dehydroxylation. In addition, cells of the novel species Bullifex porci are coccoidal or spherical under the culture conditions tested, in contrast with the usual helical shape of other members of the family Spirochaetaceae. The strain collection, called ‘Pig intestinal bacterial collection’ (PiBAC), is publicly available at www.dsmz.de/pibac and opens new avenues for functional studies of the pig gut microbiota.

show abstract

Section: Methodsmentioning

confidence: 99%

A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Other commensal microbes such as fungi have also been shown to modulate intestinal immunity during homeostasis or inflammation. [3][4][5][6][7] However, our review will focus on the effects mediated by commensal bacteria.…”

Section: Introductionmentioning

confidence: 99%

Microbial modulation of intestinal T helper cell responses and implications for disease and therapy

Geuking

Burkhard

2020

Mucosal Immunology

View full text Add to dashboard Cite

Induction of intestinal T helper cell subsets by commensal members of the intestinal microbiota is an important component of the many immune adaptations required to establish host-microbial homeostasis. Importantly, altered intestinal T helper cell profiles can have pathological consequences that are not limited to intestinal sites. Therefore, microbial-mediated modulation of the intestinal T helper cell profile could have strong therapeutic potentials. However, in order to develop microbial therapies that specifically induce the desired alterations in the intestinal T helper cell compartment one has to first gain a detailed understanding of how microbial composition and the metabolites derived or induced by the microbiota impact on intestinal T helper cell responses. Here we summarize the milestone findings in the field of microbiota-intestinal T helper cell crosstalk with a focus on the role of specific commensal bacteria and their metabolites. We discuss mechanistic mouse studies and are linking these to human studies where possible. Moreover, we highlight recent advances in the field of microbial CD4 T cell epitope mimicry in autoimmune diseases and the role of microbially-induced CD4 T cells in cancer immune checkpoint blockade therapy.

show abstract

“…Intestinal fungi have been shown to be causally implicated in microbiome assembly and immune development. 8 Accumulating findings highlighted that the gut mycobiota can strongly influence the host immune system and this interaction is linked to bacteria activities. 9,10 Recent observations of the direct and indirect effects of fungal microbiota on various GI diseases have stimulated further investigation of the mycobiota composition and ways of regulating its diversity.…”

mentioning

confidence: 99%

Alterations in Fecal Fungal Microbiome of Patients With COVID-19 During Time of Hospitalization until Discharge

et al. 2020

View full text Add to dashboard Cite

See Covering the Cover synopsis on page 1193. BACKGROUND & AIMS: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects intestinal cells, and might affect the intestinal microbiota. We investigated changes in the fecal fungal microbiomes (mycobiome) of patients with SARS-CoV-2 infection during hospitalization and on recovery. METHODS: We performed deep shotgun metagenomic sequencing analysis of fecal samples from 30 patients with coronavirus disease 2019 (COVID-19) in Hong Kong, from February 5 through May 12, 2020. Fecal samples were collected 2 to 3 times per week from time of hospitalization until discharge. We compared fecal mycobiome compositions of patients with COVID-19 with those from 9 subjects with community-acquired pneumonia and 30 healthy individuals (controls). We assessed fecal mycobiome profiles throughout time of hospitalization until clearance of SARS-CoV-2 from nasopharyngeal samples. RESULTS: Patients with COVID-19 had significant alterations in their fecal mycobiomes compared with controls, characterized by enrichment of Candia albicans and a highly heterogeneous mycobiome configuration, at time of hospitalization. Although fecal mycobiomes of 22 patients with COVID-19 did not differ significantly from those of controls during times of hospitalization, 8 of 30 patients with COVID-19 had continued significant differences in fecal mycobiome composition, through the last sample collected. The diversity of the fecal mycobiome of the last sample collected from patients with COVID-19 was 2.5-fold higher than that of controls (P < .05). Samples collected at all timepoints from patients with COVID-19 had increased proportions of opportunistic fungal pathogens, Candida albicans, Candida auris, and Aspergillus flavus compared with controls. Two respiratory-associated fungal pathogens, A. flavus and

show abstract

Intestinal fungi are causally implicated in microbiome assembly and immune development in mice

Cited by 165 publications

References 67 publications

A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity

A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity

Microbial modulation of intestinal T helper cell responses and implications for disease and therapy

Alterations in Fecal Fungal Microbiome of Patients With COVID-19 During Time of Hospitalization until Discharge

Contact Info

Product

Resources

About