【Nature sub-issue】Two articles in a row! Ma Yingfei's team excavated human intestinal archaea virus; Development of high-throughput preparation of chassis bacteriophages

This article is the original of Translational Medicine Network, please indicate the source for reprinting

Author: Mia

The human gut microbiome has been extensively explored, while archaeal viruses remain largely unknown
.
Recently, Ma Yingfei's team from Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences conducted a comprehensive analysis
of archaeal viruses and existing virus sets from the human intestinal metagenomics.

Recently, the team of Ma Yingfei of Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, published a research paper
entitled "Metagenomic analysis reveals unexplored diversity of archaeal virome in the human gut" in Nature Communications 。 The study found a high diversity of human gut archaea and archaeal viruses, and this study will help to better characterize archaeal viruses in the human gut and their archaeal hosts, and provide a complementary view
of the human gut microbiome.

https://doi.
org/10.
1038/s41467-022-35735-y

In addition, Ma Yingfei's team recently published a high-throughput method
for preparing chassis bacteriophages.
The team developed an iterative phage genome simplification (CiPGr) method based on CRISPR/cas9, which successfully simplified four different tailed phage (T7, T4, seszw, and selz) genomes, resulting in their chassis phages, non-essential gene sets, and genomic simplified phages
with stronger infection capabilities than wild-type infections.

https://doi.
org/10.
1093/nar/gkac1168

Human enteric archaea viruses have rarely been studied

 01 

The human gut microbiota is closely
related to human health.
In addition to the major bacterial components, non-bacterial members of the gut microbiota (archaea, fungi, and viruses) are known to play important roles
in microbiome dynamics and human physiology, immunity, disease, and more.
Archaea are also one of the symbiotic microorganisms that live in other organ systems of the human body, commonly found in the respiratory tract, mouth, and skin
.
However, human-related archaea are often overlooked because they are relatively low in abundance compared to bacteria and most are not
cultureable.

Microbial viruses control the composition and metabolism
of microbial communities.
To date, the dynamics of bacterial viruses in the human gut have been studied in detail, but few studies have reported the discovery of human enteric archaeal viruses, which remain very mysterious
.
In this study, the researchers used culture-independent methods, such as next-generation sequencing, to help capture their identities to perform extensive assessments
of the human archaeome and archaeal viral me.

Key findings

 02 

The researchers used spacer sequences and viral signatures from the archaeal CRISPR-Cas system to explore archaeal viruses
in the human gut.
First, large-scale identification
of archaeal genome contigs of 2971 metagenomics from previously published studies was performed.
The researchers then obtained spacers
from 1162 archaeal genomes from the identified archaeal genome contigs and UHGG (Unified Human Gastrointestinal Genome).
Based on archaeal spacer collection and protein homologous signatures present in archaeal viruses, this study established a detection pipeline for archaeal viruses and obtained 1279 archaeal viruses
in the human gut.

Of all the enteric archaeal viruses identified, M.
smithii archaea virus has the most functional diversity, containing a total of 1034 proteins with different functions, including those related to structure, packaging, cleavage, DNA binding, and replication, while some other archaeal viruses lack functional proteins
specific to these viruses 。 In addition, the research team used CheckV to conduct genome-wide testing of representative sequences of 36 archaeal viruses in the Human Intestinal Archaea Virus Database (HGAVD), and found that a total of 23 sequences carried the PeiW (pseudomurein endoisopeptidase) gene, indicating the importance of the PeiW gene for viral infection of
methanogenic archaea.

Functional characteristics of the HGAVD virus

Research significance

 03 

In summary, in this study, the research team conducted comprehensive metagenomic data mining of archaea and archaeal viruses in the human gut, revealing the diversity
of archaeal viruses and archaea in the human gut.
The large diversity of untapped archaeal viruses in the human gut and the new virus species found in HGAVD fill the gap in this field and serve as an extension
of human enteric archaeal viruses.
The research data, along with bacteria and bacterial phages, will provide a complementary view of the human enterovirus population, helping us better understand the human enteric ecosystem
.

Resources:

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https://academic.
oup.
com/nar/article/50/22/13183/6895194

Note: This article is intended to introduce the progress of medical research and cannot be used as a reference
for treatment options.
If you need health guidance, please go to a regular hospital
.

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