Single Amplified Genome Catalog Reveals the Dynamics of Mobilome and Resistome in the Human Microbiome DOI Creative Commons
Tetsuro Kawano-Sugaya,

Koji Arikawa,

Tatsuya Saeki

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 7, 2023

Abstract The increase in metagenome-assembled genomes (MAGs) has significantly advanced our understanding of the functional characterization and taxonomic assignment within human microbiome. However, MAGs, as population consensus genomes, often mask heterogeneity among species strains, thereby obfuscating precise relationships between microbial hosts mobile genetic elements (MGEs). In contrast, single amplified (SAGs) derived via single-cell genome sequencing can capture individual genomic content, including MGEs. We present bbsag20 dataset, which encompasses 17,202 human-associated prokaryotic SAGs 869 spanning 647 gut 312 oral bacterial species. revealed diverse lineages MGEs with a broad host range that were absent MAGs traced translocation bacteria to gut. Importantly, linked mobilomes resistomes meticulously charted dynamic network antibiotic resistance genes (ARGs) on MGEs, pinpointing potential ARG reservoirs community.

Language: Английский

High throughput single cell metagenomic sequencing with semi-permeable capsules: unraveling microbial diversity at the single-cell level in sewage and fecal microbiomes DOI Creative Commons
Meilee Ling, Judit Szarvas,

Vaida Kurmauskaitė

et al.

Frontiers in Microbiology, Journal Year: 2025, Volume and Issue: 15

Published: Feb. 4, 2025

Single-cell sequencing may serve as a powerful complementary technique to shotgun metagenomics study microbiomes. This emerging technology allows the separation of complex microbial communities into individual bacterial cells, enabling high-throughput genetic material from thousands singular cells in parallel. Here, we validated use microfluidics and semi-permeable capsules (SPCs) (Atrandi) isolate sewage pig fecal samples. Our method involves extracting amplifying single DNA within SPCs, followed by combinatorial split-and-pool single-amplified genome (SAG) barcoding short-read sequencing. We tested two different approaches with numbers SPCs same sample for each run. Using deep approach, detected 1,796 1,220 SAGs, which 576 599 were used further analysis one sample, respectively. In shallow data, aimed 10-times more 12,731 17,909 2,456 1,599 samples, Additionally, identified top 10 antimicrobial resistance genes (ARGs) both feces samples linked them their host species.

Language: Английский

Citations

0
Host–microbiota interaction during cancer progression from bulk to single‐cell level DOI Creative Commons

Yongjing Ma,

Run‐Ze Zhu,

Ning‐Ning Liu

et al.

Clinical and Translational Discovery, Journal Year: 2024, Volume and Issue: 4(1)

Published: Jan. 28, 2024

Abstract Background Cancer, a global threat to human health, refers large crowd of lethal diseases that can start in almost all tissues or organs our body when abnormal cells grow uncontrollably and beyond their usual boundaries, followed by invading adjacent normal spreading distant organs. Recently, substantial evidence has demonstrated polymorphic microbiome as an emerging cancer characteristic present variety tumour types. By releasing metabolites other signalling molecules, microbiota affect immune cell differentiation activity, including both innate adaptive immunological responses, well the growth multiplication cells. It was now employed biomarker predict patients’ survival rate degree progression. Main To investigate underlying mechanism technology development how influence microenvironment subsequently progression, we have carried out systematic literature review about from bulk single‐cell level. Conclusions Here, provide overview current advancements host–microbiota interactions during progression level discuss challenges opportunities future, looking forward ascertain specific activity different somatic types with without existence various multi‐kingdom by‐products supply holistic elaborate investigation host‐microbiota interaction cancer.

Language: Английский

Citations

2
A single amplified genome catalog reveals the dynamics of mobilome and resistome in the human microbiome DOI Creative Commons
Tetsuro Kawano-Sugaya,

Koji Arikawa,

Tatsuya Saeki

et al.

Microbiome, Journal Year: 2024, Volume and Issue: 12(1)

Published: Oct. 2, 2024

The increase in metagenome-assembled genomes (MAGs) has advanced our understanding of the functional characterization and taxonomic assignment within human microbiome. However, MAGs, as population consensus genomes, often aggregate heterogeneity among species strains, thereby obfuscating precise relationships between microbial hosts mobile genetic elements (MGEs). In contrast, single amplified (SAGs) derived via single-cell genome sequencing can capture individual genomic content, including MGEs.

Language: Английский

Citations

2
Recent Innovations and Technical Advances in High‐Throughput Parallel Single‐Cell Whole‐Genome Sequencing Methods DOI
Yi Qiao, Tianguang Cheng,

Zikun Miao

et al.

Small Methods, Journal Year: 2024, Volume and Issue: unknown

Published: July 9, 2024

Abstract Single‐cell whole‐genome sequencing (scWGS) detects cell heterogeneity at the aspect of genomic variations, which are inheritable and play an important role in life processes such as aging cancer progression. The recent explosive development high‐throughput single‐cell methods has enabled high‐performance detection through a vast number novel strategies. Despite limitation on total cost, technical advances made for higher genome coverage, parallel throughput, level integration. This review highlights advancements scWGS aspects strategies design, data efficiency, handling platforms, their applications human genome. experimental innovations, remaining challenges, perspectives summarized discussed.

Language: Английский

Citations

0
Single-Molecule Barcoding Technology for Single-Cell Genomics DOI Creative Commons
Ivan García-Bassets,

Guoya Mo,

Yu Xia

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 13, 2024

ABSTRACT Recent advances in barcoding technologies have significantly enhanced the scalability of single-cell genomic experiments. However, large-scale experiments are still rare due to high costs, complex logistics, and laborintensive procedures. To facilitate routine application largest scalability, it is critical simplify production use reagents. Here, we introduce AmpliDrop, a technology that initiates process using pool inexpensive single-copy barcodes integrates barcode multiplicity generation with tagging cellular content into single reaction driven by DNA polymerase during library preparation. The reactions compartmentalized an electronic pipette or robotic standalone liquid handling system. These innovations eliminate need for barcoded beads combinatorial indexing workflows provide flexibility wide range scales tube formats, as well compatibility automation. We show AmpliDrop capable capturing transcriptomes chromatin accessibility, can also be adapted user-customized applications, including antibody-based protein detection, bacterial viral CRISPR perturbations without dual guide RNA-expression vectors. validated investigating influence short-term static culturing on cell composition human forebrain organoids, revealing metabolic reprogramming lineage progenitors.

Language: Английский

Citations

0
Droplet Microfluidic Systems for Multistep Single-Cell Sequencing Assays DOI
Zofia Olszewska, Adam Pyzik,

Marcin Malkowski

et al.

Bioanalysis, Journal Year: 2024, Volume and Issue: unknown, P. 495 - 520

Published: Jan. 1, 2024

Language: Английский

Citations

0
Single Amplified Genome Catalog Reveals the Dynamics of Mobilome and Resistome in the Human Microbiome DOI Creative Commons
Tetsuro Kawano-Sugaya,

Koji Arikawa,

Tatsuya Saeki

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 7, 2023

Abstract The increase in metagenome-assembled genomes (MAGs) has significantly advanced our understanding of the functional characterization and taxonomic assignment within human microbiome. However, MAGs, as population consensus genomes, often mask heterogeneity among species strains, thereby obfuscating precise relationships between microbial hosts mobile genetic elements (MGEs). In contrast, single amplified (SAGs) derived via single-cell genome sequencing can capture individual genomic content, including MGEs. We present bbsag20 dataset, which encompasses 17,202 human-associated prokaryotic SAGs 869 spanning 647 gut 312 oral bacterial species. revealed diverse lineages MGEs with a broad host range that were absent MAGs traced translocation bacteria to gut. Importantly, linked mobilomes resistomes meticulously charted dynamic network antibiotic resistance genes (ARGs) on MGEs, pinpointing potential ARG reservoirs community.

Language: Английский

Citations

0