Beyond Just Bacteria: Functional Biomes in the Gut Ecosystem Including Virome, Mycobiome, Archaeome and Helminths

Vemuri, Ravichandra; Shankar, Esaki Muthu; Chieppa, Marcello; Eri, Rajaraman; Kavanagh, Kylie

doi:10.3390/microorganisms8040483

Cited by 116 publications

(84 citation statements)

References 155 publications

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“…The elderly gut is home to three main phyla, namely Ascomycota, Basidiomycota and Zygomycota. The most prevalent genera among the elderly Danes were Penicillium , followed by Candida , and Aspergillus (Supplementary Table 1), as previously described in preliminary studies using similar cohort [39]– [41].…”

Section: Resultsmentioning

confidence: 55%

Gut Mycobiome Dysbiosis is Linked to Hypertriglyceridemia Among Home Dwelling Elderly Danes

Ahmad

Castro‐Mejía

Krych

et al. 2020

Preprint

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24 25 26 Email addresses: 27 HFA fauzanahmad@ump.edu.my 28 JLC jcame@food.ku.dk 29 ŁK krych@food.ku.dk 30 BK bzo@food.ku.dk 31 WK wk@envs.au.dk 32 RLB r.bechshoeft@gmail.com 33 SR s.reitelseder@gmail.com 34 GWH grith.westergaard.hoejfeldt.01@regionh.dk 35 SBE se@food.ku.dk 36 LH l.holm@bham.ac.uk 37 KF karoline.faust@kuleuven.be 38 DSN dn@food.ku.dk 39 40 41 42 43 44 45 ABSTRACT 46 Gut microbial dysbiosis have been in the etiology of a number of diseases, yet 47 the presence of fungal communities and their possible association with host health are 48 little understood. This study attempts to identify gut microbial fungal associations 49 with the progression of atherogenic dyslipidemia in a population of older adults by 50 investigating the interplay between dietary intake, gut mycobiome composition, 51 plasma and fecal metabolome and anthropometric/body-composition measurements of 52 100 Danes aged 65 to 81 (69.57  3.64) years. The gut mycobiome composition were 53 determined by high-throughput sequencing of internal transcribed spacer (ITS2) gene 54 amplicons, while the plasma and fecal metabolome was determined by GC-TOF-MS. 55 The gut microbiome of the subjects investigated is home to three main eukaryotic 56 phyla, namely Ascomycota, Basidiomycota and Zygomycota, with genera 57 Penicillium, Candida, and Aspergillus being particularly common. 58 Hypertriglyceridemia was associated with fewer observed fungal species, and Bray-59 Curtis dissimilarity matrix-based analysis showed significant (P<0.05) clustering 60 according to fasting levels of circulating plasma triglycerides (Tg) and very low-61 density lipoprotein (VLDL) cholesterol fasting levels, respectively. Interestingly, 62 neither hypertriglyceridemia nor elevated VLDL levels were reflected in the 63 prokaryotic component of the gut microbiome as determined by 16S rRNA gene 64 amplicon sequencing. Higher levels of Tg and VLDL cholesterol significantly 65 associates with increased relative abundance of genus Penicillium, possibly mediated 66 by a higher dietary fat intake (ANOVA, P<0.05), and Aspergillus and Guehomyces 67 were positively associated with SCFAs groups. Collectively, these findings suggest 68 that in older adults' gut mycobiome dysbiosis is associated with hypertriglyceridemia, 69 a known risk factor for development of cardiovascular disease. 70 71 Keywords: older-adults, hypertriglyceridemia, dysbiosis, gut mycobiome, host 72 metabolome, triglyceride, VLDL and dietary fat intake 73 74 75 93 dyslipidaemia in both men and women older than 65 years, as compared to younger 94 individuals [16]. Further, elevated triglycerides (Tg) and very low density level 95 (VLDL) cholesterol levels have been associated with subclinical atherosclerosis and 96 dubbed as independent risk factors for CVD [17]. Several large studies suggest that 97 hypertriglyceridemia is related to increased levels of remnant lipoproteins in 98 promoting atherogenesis [18], [19]. The possible mechanisms for this association 99 include excessive free fatty acid release, product...

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Section: Resultsmentioning

confidence: 55%

Gut Mycobiome Dysbiosis is Linked to Hypertriglyceridemia Among Home Dwelling Elderly Danes

Ahmad

Castro‐Mejía

Krych

et al. 2020

Preprint

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“…A larger sample size is required for future studies to account for the high degree of inter-individual variability in the intestinal virobiota, to get a complete picture of the virome of CF patients, and minimise the influence of outliers (which is controlled for using the ANCOM analysis [49]). Although the percentage of predictions mapped to functional terms is small, a recent review of human gut virome literature identified 18 studies, none of which performed a functional annotation [50]. Bacterial contamination rates in our sequencing data were quite varied and could require optimisation, however the level is on par with other current studies [27,28].…”

Section: Discussionmentioning

confidence: 93%

The intestinal virome in children with cystic fibrosis differs from healthy controls

et al. 2020

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Intestinal bacterial dysbiosis is evident in children with cystic fibrosis (CF) and intestinal viruses may be contributory, given their influence on bacterial species diversity and biochemical cycles. We performed a prospective, case-control study on children with CF and age and gender matched healthy controls (HC), to investigate the composition and function of intestinal viral communities. Stool samples were enriched for viral DNA and RNA by viral extraction, random amplification and purification before sequencing (Illumina MiSeq). Taxonomic assignment of viruses was performed using Vipie. Functional annotation was performed using Virsorter. Inflammation was measured by calprotectin and M2-pyruvate kinase (M2-PK). Eight CF and eight HC subjects were included (50% male, mean age 6.9 ± 3.0 and 6.4 ± 5.3 years, respectively, p = 0.8). All CF subjects were pancreatic insufficient. Regarding the intestinal virome, no difference in Shannon index between CF and HC was identified. Taxonomy-based beta-diversity (presence-absence Bray-Curtis dissimilarity) was significantly different between CF and HC (R 2 = 0.12, p = 0.001). Myoviridae, Faecalibacterium phage FP Taranis and unclassified Gokushovirinae were significantly decreased in CF compared with HC (q<0.05). In children with CF (compared to HC), the relative abundance of genes annotated to (i) a peptidoglycan-binding domain of the peptidoglycan hydrolases (COG3409) was significantly increased (q<0.05) and (ii) capsid protein (F protein) (PF02305.16) was significantly decreased (q<0.05). Picornavirales, Picornaviridae, and Enterovirus were found to positively correlate with weight and BMI (r = 0.84, q = 0.01). Single-stranded DNA viruses negatively correlated with M2-PK (r =-0.86, q = 0.048). Children with CF have an altered intestinal virome compared to well-matched HC, with both taxonomic and predicted functional changes. Further exploration of Faecalibacterium phages, Gokushovirinae and phage lysins are warranted. Intestinal viruses and their functions may

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“…Gut virome genes are also implicated in human metabolism, inflammation and carcinogenesis modulation [114]. Recent evidence points out to a new role of bacteriophages in liver metabolism and immune response regulation in humans [115].…”

Section: Gut Virome and Liver Diseases At The Time Of Sars-cov-2 Pandmentioning

confidence: 99%

Gut Microbiota and Liver Interaction through Immune System Cross-Talk: A Comprehensive Review at the Time of the SARS-CoV-2 Pandemic

Scarpellini

Fagoonee

Rinninella

et al. 2020

JCM

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Background and aims: The gut microbiota is a complex ecosystem containing bacteria, viruses, fungi, yeasts and other single-celled organisms. It is involved in the development and maintenance of both innate and systemic immunity of the body. Emerging evidence has shown its role in liver diseases through the immune system cross-talk. We review herein literature data regarding the triangular interaction between gut microbiota, immune system and liver in health and disease. Methods: We conducted a search on the main medical databases for original articles, reviews, meta-analyses, randomized clinical trials and case series using the following keywords and acronyms and their associations: gut microbiota, microbiome, gut virome, immunity, gastrointestinal-associated lymphoid tissue (GALT), non-alcoholic fatty liver disease (NAFLD), non-alcoholic steato-hepatitis (NASH), alcoholic liver disease, liver cirrhosis, hepatocellular carcinoma. Results: The gut microbiota consists of microorganisms that educate our systemic immunity through GALT and non-GALT interactions. The latter maintain health but are also involved in the pathophysiology and in the outcome of several liver diseases, particularly those with metabolic, toxic or immune-mediated etiology. In this context, gut virome has an emerging role in liver diseases and needs to be further investigated, especially due to the link reported between severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection and hepatic dysfunctions. Conclusions: Changes in gut microbiota composition and alterations in the immune system response are involved in the pathogenesis of metabolic and immune-mediated liver diseases.

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Beyond Just Bacteria: Functional Biomes in the Gut Ecosystem Including Virome, Mycobiome, Archaeome and Helminths

Cited by 116 publications

References 155 publications

Gut Mycobiome Dysbiosis is Linked to Hypertriglyceridemia Among Home Dwelling Elderly Danes

Gut Mycobiome Dysbiosis is Linked to Hypertriglyceridemia Among Home Dwelling Elderly Danes

The intestinal virome in children with cystic fibrosis differs from healthy controls

Gut Microbiota and Liver Interaction through Immune System Cross-Talk: A Comprehensive Review at the Time of the SARS-CoV-2 Pandemic

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