The role of virome in the gastrointestinal tract and beyond

Tiamani, Kawtar; Luo, Shiqi; Schulz, Sarah; Xue, Jinling; Costa, Rita; Mirzaei, Mohammadali Khan; Deng, Li

doi:10.1093/femsre/fuac027

Cited by 24 publications

(21 citation statements)

References 147 publications

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“…More precisely, the intestinal microbiome is basically composed of multiple bacterial species (~50 bacterial phyla) in which Bacteroidetes and Firmicutes are the dominant phyla in a healthy human gut. Additionally, Proteobacteria and Actinobacteria are found in abundance, whereas the genera Bifidobacterium , Escherichia , Clostridium, and Akkermansia are also detected at lower levels [ 9 , 71 ]. Moreover, most studies support that the human gut archaeome includes two methanogenic classes of Archaea: the Methanobacteriales and the Methanomassiliicoccales.…”

Section: The Role Of the Gastrointestinal Tract Microbiota In Human H...mentioning

confidence: 99%

“…Finally, the gut also harbors viruses which contribute to homeostasis in human physiology. Briefly, DNA bacteriophages, such as Caudovirales and members of other families such as Myoviridae and Siphoviridae, dominate in the gut virome, while Circovirus and a small number of other eukaryotic and archaea viruses are present [ 71 , 82 , 83 , 84 ].…”

Section: The Role Of the Gastrointestinal Tract Microbiota In Human H...mentioning

confidence: 99%

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Unveiling the Human Gastrointestinal Tract Microbiome: The Past, Present, and Future of Metagenomics

2023

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Over 1014 symbiotic microorganisms are present in a healthy human body and are responsible for the synthesis of vital vitamins and amino acids, mediating cellular pathways and supporting immunity. However, the deregulation of microbial dynamics can provoke diverse human diseases such as diabetes, human cancers, cardiovascular diseases, and neurological disorders. The human gastrointestinal tract constitutes a hospitable environment in which a plethora of microbes, including diverse species of archaea, bacteria, fungi, and microeukaryotes as well as viruses, inhabit. In particular, the gut microbiome is the largest microbiome community in the human body and has drawn for decades the attention of scientists for its significance in medical microbiology. Revolutions in sequencing techniques, including 16S rRNA and ITS amplicon sequencing and whole genome sequencing, facilitate the detection of microbiomes and have opened new vistas in the study of human microbiota. Especially, the flourishing fields of metagenomics and metatranscriptomics aim to detect all genomes and transcriptomes that are retrieved from environmental and human samples. The present review highlights the complexity of the gastrointestinal tract microbiome and deciphers its implication not only in cellular homeostasis but also in human diseases. Finally, a thorough description of the widely used microbiome detection methods is discussed.

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Section: The Role Of the Gastrointestinal Tract Microbiota In Human H...mentioning

confidence: 99%

Section: The Role Of the Gastrointestinal Tract Microbiota In Human H...mentioning

confidence: 99%

Unveiling the Human Gastrointestinal Tract Microbiome: The Past, Present, and Future of Metagenomics

2023

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“…The interactions between gut bacteria and phages are complex and gut microbiome diversity is linked to gut virome diversity, hence making the gut virome an important component in health and disease [8,9]. Microbiome abundances and diversity are predictive of virome richness and diversity [10] and the number of virus-like particles (VLP) in feces has been estimated to be between 10 9 and 10 10 VLP/g [11][12][13][14].…”

Section: Introductionmentioning

confidence: 99%

“…The healthy adult gut virome is highly personal and stable over time within each individual [11,19,20]. Phages belonging to the order Caudovirales are the most dominant in the human gut [8,9,21,22]. The impact of phageome on the composition and function of the gut microbiota has been suggested to have important consequences for health and outcome of FMT or FVT treatments [2,[23][24][25][26].…”

Section: Introductionmentioning

confidence: 99%

Reproducible chemostat cultures to eliminate eukaryotic viruses from fecal transplant material

Adamberg

Rasmussen

Larsen

et al. 2023

Preprint

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The effect of fecal microbiota transplantation (FMT) on various gut-related diseases is intensively investigated in clinical trials. In addition to bacteria, the gut microbiome also contains eukaryotic, archaeal, and bacterial viruses (bacteriophages, in short phages), which collectively is referred to, as the gut virome. Application of FMT in clinical studies is associated with a potential risk for the recipient of transferring infectious eukaryotic viruses or bacteria, despite strict screening procedure of the donor material. A safer and more targeted method to modulate the gut microbiota is therefore needed to extend the application width of FMT. Emerging evidence suggests that gut phages play a key role in maintaining a balanced gut microbiome as well as in FMT efficacy. Thus, a phageome from a cultured fecal donor microbiome may be a more efficient alternative to modulate the gut bacteriome than FMT. Here, we analyzed the dynamic changes of the viromes of mice cecal and human fecal cultures in chemostat cultures. Sequencing results showed that the relative abundance of eukaryotic viruses remarkably decreased during continuous cultivation, likely due to the lack of eukaryotic hosts. The corresponding phageome profiles showed dilution rate dependency, a reproducibility between biological replicates, and to maintain a high and stable diversity of phages although being different from the inoculum phageome. This proof-of-concept study may constitute the first step of developing therapeutic tools to target a broad spectrum of gut-related diseases and thereby replacing FMT with a safer phage-mediated therapy.

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“…Phages are also abundant within humans and animals ( Cao et al. 2022 ; Tiamani et al. 2022 ) and play key ecological roles in regulating the microbial community within these niches ( Liang and Bushman 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Coevolutionary phage training and Joint application delays the emergence of phage resistance in Pseudomonas aeruginosa

Wang,

Wei,

Jiang

et al. 2023

Virus Evolution

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Antibiotic-resistant bacteria are current threats to available antibiotic therapies, and this has renewed interest in the therapeutic use of phage as an alternative. However, development of phage resistance has led to unsuccessful therapeutic outcomes. In the current study, we applied phage training to minimize bacterial phage resistance and to improve treatment outcome by adapting the phage to their target hosts during co-evolution. We isolated and characterized a novel Pseudomonas aeruginosa N4-like lytic phage (PWJ) from wastewater in Yangzhou, China. PWJ is a double-stranded DNA podovirus that can efficiently lyse the model strain ATCC 27,853 and opportunistic pathogen PAO1. Genome sequencing of PWJ revealed features similar to those of the N4-like P. aeruginosa phage YH6. We used PWJ to screen for an evolved trained phage (WJ_Ev14) that restored infectivity to PWJ phage bacterial resisters. BLASTN analysis revealed that WJ_Ev14 is identical to its ancestor PWJ except for the amino acid substitution R1051S in its tail fiber protein. Moreover, phage adsorption tests and transmission electron microscopy of resistant bacteria demonstrated that the R1051S substitution was most likely the reason WJ_Ev14 could re-adsorb and regain infectivity. Furthermore, phage therapy assays in vitro and in a mouse P. aeruginosa lung infection model demonstrated that PWJ treatment resulted in improved clinical results and a reduction in lung bacterial load whereas the joint phage cocktail (PWJ+ WJ_Ev14) was better able to delay the emergence of resister bacteria. The phage cocktail (PWJ +WJ_Ev14) represents a promising candidate for inclusion in phage cocktails developed for clinical applications.

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The role of virome in the gastrointestinal tract and beyond

Cited by 24 publications

References 147 publications

Unveiling the Human Gastrointestinal Tract Microbiome: The Past, Present, and Future of Metagenomics

Unveiling the Human Gastrointestinal Tract Microbiome: The Past, Present, and Future of Metagenomics

Reproducible chemostat cultures to eliminate eukaryotic viruses from fecal transplant material

Coevolutionary phage training and Joint application delays the emergence of phage resistance in Pseudomonas aeruginosa

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