Review
Immunology
Bhoomi Madhu, Brittany M. Miller, Maayan Levy
Summary: Research in the past decade has shown that the composition and function of the gut microbiome have a significant impact on intestinal and extra-intestinal diseases. While a common pattern of microbial dysbiosis associated with these diseases has not been identified, disrupted spatial organization of the gut microbiome is often a common feature in disease pathogenesis. Therefore, recent focus has shifted towards understanding the gut microbiome in a spatial context.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Ecology
Manolito G. Torralba, Claire Kuelbs, Kelvin Jens Moncera, Rhonda Roby, Karen E. Nelson
Summary: The study of microbial communities on artwork using molecular biology methods has immense potential in identifying potentially damaging species and addressing challenges in restoration and preservation efforts. Different types of artwork, such as paintings on wood, paintings on canvases, and stone sculptures, were found to have differing bacterial communities, with certain oxidase-positive genera potentially responsible for deterioration and fading. This genomics-based approach provides advantages in identifying harmful species that may not be detected using traditional methods and in overcoming challenges in preservation and restoration.
Article
Microbiology
Masato Kogawa, Yohei Nishikawa, Tatsuya Saeki, Takuya Yoda, Koji Arikawa, Haruko Takeyama, Masahito Hosokawa
Summary: Single-cell genomics is a promising approach for studying uncultured bacteria. In this study, a single-cell amplified genome long-read assembly (scALA) workflow was developed to construct complete circular single-amplified bacterial genomes. Through scALA, 16 complete circular genomes of specific bacteria were obtained from human fecal samples, providing insights into microbial evolution, adaptation to environmental changes, and interactions with hosts.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Melanie A. Brennan, Adam Z. Rosenthal
Summary: Clonal bacterial populations exhibit various forms of heterogeneity, which impact productivity and disease virulence. Single-cell RNA sequencing (scRNA-seq) is considered a valuable approach to examine this heterogeneity, but current methods face challenges when applied to bacteria.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Medical Laboratory Technology
Xue Bai, Yuxuan Li, Xuemei Zeng, Qiang Zhao, Zhiwei Zhang
Summary: The emergence of single-cell sequencing technology has effectively addressed the issue of tumor cell heterogeneity, providing important basis for correctly classifying tumor cells and revealing their molecular level changes.
CLINICA CHIMICA ACTA
(2021)
Article
Biology
Hanako Ono, Yasuhito Arai, Eisaku Furukawa, Daichi Narushima, Tetsuya Matsuura, Hiromi Nakamura, Daisuke Shiokawa, Momoko Nagai, Toshio Imai, Koshi Mimori, Koji Okamoto, Yoshitaka Hippo, Tatsuhiro Shibata, Mamoru Kato
Summary: This study investigated the dynamics of intra-tumor heterogeneity in a mouse colorectal cancer model through single-cell exome and transcriptome sequencing. The results showed an increase in transcriptome diversity and a decrease in genome diversity after serial transplantation. The emergence of new transcriptional subpopulations was found to be key for cancer cells to adapt to microenvironmental changes with genetic alterations at later tumor stages.
Article
Multidisciplinary Sciences
Ori Heyman, Dror Yehezkel, Camilla Ciolli Mattioli, Neta Blumberger, Gili Rosenberg, Aryeh Solomon, Dotan Hoffman, Noa Bossel Ben-Moshe, Roi Avraham
Summary: Encounters between host cells and intracellular bacterial pathogens lead to complex phenotypes that determine the outcome of infection. Single-cell RNA sequencing (scRNA-seq) has limited capacity to analyze the role of bacterial factors. The scPAIR-seq method developed in this study enables functional analysis of mutant-dependent changes in host transcriptomes, providing insights into bacterial virulence strategies and their interplay with host defense strategies.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Immunology
Fangyue Chen, Jun Yang, Youxiang Guo, Dongwei Su, Yuan Sheng, Yanmei Wu
Summary: This study found a correlation between tumor microbiome and cancer metabolic activity in breast cancer patients. It also predicted overall survival and identified associations with gene mutation, immune cell composition, and response to immunotherapy. Overall, it sheds light on the potential role of metabolism-related microbiome in breast cancer patients and suggests new treatment possibilities through further investigation of metabolic disturbances in host and intratumor microbial cells.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Microbiology
Kuanguan Huang, Jie Wang, Junhao Huang, Shouke Zhang, Alfried P. Vogler, Quanquan Liu, Yongchun Li, Maowei Yang, You Li, Xuguo Zhou
Summary: In this study, gut microbiota of bamboo-feeding insects were examined to understand their convergent adaptation to extreme diet specialization. Results showed that while both phylogeny and diet can influence the gut microbiome composition, phylogeny primarily drives the convergent adaptation to a highly specialized diet in insects feeding on bamboo.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Ecology
Manolito G. Torralba, Gajender Aleti, Weizhong Li, Kelvin Jens Moncera, Yi-Han Lin, Yanbao Yu, Michal M. Masternak, Wojciech Golusinski, Pawel Golusinski, Katarzyna Lamperska, Anna Edlund, Marcelo Freire, Karen E. Nelson
Summary: The study found a higher number of Fusobacteria, Bacteroidetes, and Firmicutes in oral squamous cell carcinoma (OSCC) tumor tissue, with an increase of Prevotella in saliva from OSCC patients and a prevalence of Corynebacterium in healthy subjects. Additionally, adhesion and virulence factors associated with Streptococcus gordonii and Fusobacterium genera were detected in OSCC tissues, suggesting potential biomarkers for disease progression.
Article
Biology
Brian D. Williamson, James P. Hughes, Amy D. Willis
Summary: The paper proposes a method to jointly model relative abundance data for many taxa and absolute abundance data for a subset of taxa, providing point and interval estimates for all taxa. By modeling taxon-specific efficiencies, the method substantially reduces estimation error for absolute abundance and controls the coverage of interval estimators. The performance of the proposed method is demonstrated through simulation studies, studies on the effect of HIV acquisition on microbial abundances, and sensitivity studies.
Article
Plant Sciences
Siyuan Ma, Yubin Lin, Yongqiang Qin, Xiaoping Diao, Peng Li
Summary: By studying the rhizosphere microbiota of areca palm at different growth stages in Wanning, Hainan province, significant shifts in the taxonomic composition of bacteria and fungi were observed, revealing dominant microbial genera and those reaching significant levels. An interaction network of bacterial and fungal OTUs was constructed, showing that bacterial OTUs exhibited more extensive interactions than fungal OTUs, providing a basis for exploring microbial associations and maintaining the health of the areca palm.
Article
Veterinary Sciences
Wenli Li, Anna Larsen, Brianna Murphy, Priscila Fregulia
Summary: Using a model of ruminal acidosis, this study investigated changes in the liver microbiome in young calves. The results showed that calves with acidosis had lower weight gain, ruminal pH, and rumen degradation compared to the control group. Several genera, including Fibrobacter, Treponema, Lactobacillus, and Olsenella, showed significant abundance changes in the liver of acidosis calves. Additionally, there were concurrent abundance changes in some genera between the liver and rumen tissues, indicating potential crosstalk between these microbial communities. The study also identified new actively transcribed microbial taxa in the liver.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Microbiology
Hoon Je Seong, Simon Roux, Chung Yeon Hwang, Woo Jun Sul
Summary: The distribution patterns of microbial epigenetic marks in the ocean microbiome were analyzed through genome-centric metagenomics, revealing that DNA methylation patterns are associated with ecological changes and virus-host dynamics in the ocean microbiome.
Article
Entomology
Hai-Bo Pan, Mu-Yu Li, Wei Wu, Zheng-Liang Wang, Xiao-Ping Yu
Summary: The study revealed that different host plants significantly influence the microbial composition of small brown planthoppers, leading to changes in microbial community structure. Significant differences in abundance were observed in both bacteria and fungi among small brown planthopper populations feeding on different host plants.
JOURNAL OF ECONOMIC ENTOMOLOGY
(2021)