Review
Immunology
Javier Casado, Angel Lanas, Andres Gonzalez
Summary: Two-component regulatory systems (TCRS) are important signal transduction mechanisms in bacteria that play a crucial role in bacterial viability and pathogenicity. H. pylori and C. jejuni, which are classified as high priority pathogens, express various TCRS and orphan response regulators, controlling multiple physiological processes and virulence factors. These microbial molecules hold potential as novel therapeutic targets for the development of new antibiotics.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Microbiology
Chaofang Zhong, Bingpeng Qu, Gang Hu, Kang Ning
Summary: This study revealed the pan-genome of 39 Campylobacter species, provided the most updated reconstruction of the global virulence gene pool of 39 Campylobacter species, and identified species-related virulence differences.
MICROBIOLOGY SPECTRUM
(2022)
Article
Medicine, General & Internal
Yoshiaki Usui, Yukari Taniyama, Mikiko Endo, Yuriko N. Koyanagi, Yumiko Kasugai, Isao Oze, Hidemi Ito, Issei Imoto, Tsutomu Tanaka, Masahiro Tajika, Yasumasa Niwa, Yusuke Iwasaki, Tomomi Aoi, Nozomi Hakozaki, Sadaaki Takata, Kunihiko Suzuki, Chikashi Terao, Masanori Hatakeyama, Makoto Hirata, Kokichi Sugano, Teruhiko Yoshida, Yoichiro Kamatani, Hidewaki Nakagawa, Koichi Matsuda, Yoshinori Murakami, Amanda B. Spurdle, Keitaro Matsuo, Yukihide Momozawa
Summary: This study reveals that certain genetic variants associated with Helicobacter pylori infection can increase the risk of gastric cancer. Individuals carrying these genetic variants and infected with H. pylori have an even higher risk of developing gastric cancer.
NEW ENGLAND JOURNAL OF MEDICINE
(2023)
Article
Plant Sciences
H. Busra Cagirici, Carson M. M. Andorf, Taner Z. Z. Sen
Summary: This study utilized gene co-expression networks and combined gene expression with GWAS-driven traits to uncover knowledge about genotype-phenotype relationships and transcriptional regulatory mechanisms in maize. The private-network contained most of the genes but lacked some interactions, and the core-network alone could not provide a comprehensive view of the gene regulatory network.
Article
Biochemistry & Molecular Biology
Jurgita Aksomaitiene, Aleksandr Novoslavskij, Mindaugas Malakauskas
Summary: This study characterized the antimicrobial resistance (AMR) and virulence genes of Campylobacter jejuni isolates from different sources in Lithuania using whole-genome sequencing. The results revealed diverse AMR and virulence gene profiles in C. jejuni, with different patterns of resistance to various antimicrobials. Additionally, the study identified different sequence types and clonal complexes based on core-genome MLST analysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Asher Preska Steinberg, Mingzhi Lin, Edo Kussell
Summary: Recombination plays a key role in microbial evolution and affects antibiotic resistance, antigenic variation, and adaptation to different environments. This study quantifies the impact of homologous recombination on core and accessory genes in bacteria using a computationally efficient approach. The results show that core genes have higher recombination rates compared to accessory genes, and in some bacterial species, this difference is pronounced. Additionally, gene frequency and homologous recombination rate are positively correlated in some species.
Article
Immunology
Morgane Nennig, Ann-Katrin Llarena, Malte Herold, Joel Mossong, Christian Penny, Serge Losch, Odile Tresse, Catherine Ragimbeau
Summary: A study on Campylobacter jejuni in Luxembourg revealed an unexpected endemic pattern in the genetic profiles, and tested the hypothesis of stable lineages occurrence by implementing whole genome sequencing (WGS). Results showed that regardless of the typing scheme used, epidemic or endemic signals were detected in the lineages, supporting the clonal expansion of stable genomes in the Campylobacter population.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Microbiology
You Zhou, Dike Jiang, Xueping Yao, Yan Luo, Zexiao Yang, Meishen Ren, Ge Zhang, Yuanyuan Yu, Aiping Lu, Yin Wang
Summary: Glaesserella parasuis is a gram-negative bacterium that causes fibrotic polyserositis and arthritis in pigs, significantly impacting the pig industry. The pan-genome of G. parasuis is open and shows differences in the core and accessory genomes as the number of genes increases. The genes associated with virulence and biofilm formation in G. parasuis are still unclear due to its diversity. Therefore, a pan-genome-wide association study (Pan-GWAS) was conducted on 121 strains of G. parasuis. The study revealed the core genome consists of 1,133 genes associated with cytoskeleton, virulence, and basic biological processes. The accessory genome contributes to the genetic diversity of G. parasuis. Furthermore, the study identified 142 genes associated with strong virulence traits and their involvement in metabolic pathways, signal pathways, and virulence factors for bacterial survival and biofilm formation. This research provides a foundation for further investigation into virulence and biofilm formation and offers potential targets for drug and vaccine development against G. parasuis.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Victoria Mesa, Marc Monot, Laurent Ferraris, Michel Popoff, Christelle Mazuet, Frederic Barbut, Johanne Delannoy, Bruno Dupuy, Marie-Jose Butel, Julio Aires
Summary: This study provides the closed genome assembly and functional annotation of Clostridium neonatale ATCC BAA-265(T) reference strain. Pan-genome, core-genome, and accessory genome analyses reveal the genetic diversity and plasticity of C. neonatale genomes. The findings contribute to the understanding of the biological capabilities of this species.
MICROBIAL GENOMICS
(2022)
Article
Plant Sciences
Alan E. Yocca, Patrick P. Edger
Summary: The study aims to use a machine learning model to classify genes of two grass species as core or dispensable, reducing the need for pangenome construction.
Review
Biochemistry & Molecular Biology
Junpeng Shi, Zhixi Tian, Jinsheng Lai, Xuehui Huang
Summary: Plant genomes are highly diverse and most genomic sequences are not shared among individuals. Variable DNA sequences and conserved core sequences form a more sophisticated pan-genome, representing all non-redundant DNA in a species. Advances in genome sequencing technologies have accelerated plant pan-genomics research. This review focuses on driving forces of structural variations, methodological innovations, and major successes in constructing plant pan-genomes. Efforts are also summarized towards decoding dark matter in telomere-to-telomere or gapless plant genomes. These new genome resources are expected to become new references for genetic studies and plant breeding.
Article
Microbiology
Gaurav Agarwal, Divya Choudhary, Shaun P. Stice, Brendon K. Myers, Ronald D. Gitaitis, Stephanus N. Venter, Brian H. Kvitko, Bhabesh Dutta
Summary: The study identified chromosomal and plasmid gene clusters as well as novel genes associated with pathogenicity in Pantoea ananatis through a comprehensive pan-genome wide association study. These genes play a role in the development of center rot disease in onions.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Mohamad Hazwan Fikri Khairi, Nor Azlan Nor Muhammad, Hamidun Bunawan, Abdul Munir Abdul Murad, Ahmad Bazli Ramzi
Summary: This study sequenced and annotated the genome of Ganoderma boninense, the major causal agent of basal stem rot disease in oil palm. The comparative genome analysis and construction of the pan-secretome revealed candidate effector proteins and their role in pathogenicity and host defense. Genome architecture analysis provided insights into the structure of the G. boninense genome. These findings contribute to the understanding of pathogenicity determinants and the development of molecular biomarkers for basal stem rot disease.
Article
Microbiology
Gaurav Agarwal, Ronald D. Gitaitis, Bhabesh Dutta
Summary: This study revealed the genomic structure and evolution pattern of Psi through whole genome sequencing and phylogenetic analysis, identifying pathogenicity genes of Psi in onions. Horizontal gene transfer analysis demonstrated gene transfer between different Pantoea species, with frequent gene transfer events observed between the two pathovars of Psi.
Article
Plant Sciences
Tugdem Muslu, Sezgi Biyiklioglu-Kaya, Bala Ani Akpinar, Meral Yuce, Hikmet Budak
Summary: Pan-genomes are efficient for identifying conserved and varying genomic sequences within species lineages. Studying genetic variations, such as miRNA content, can lead to the discovery of beneficial traits and insights into regulatory mechanisms. Future research could introduce these traits to different lineages or plant species to enhance survival in various environments.
Article
Biology
Claude Rispe, Fabrice Legeai, Paul D. Nabity, Rosa Fernandez, Arinder K. Arora, Patrice Baa-Puyoulet, Celeste R. Banfill, Leticia Bao, Miquel Barbera, Maryem Bouallegue, Anthony Bretaudeau, Jennifer A. Brisson, Federica Calevro, Pierre Capy, Olivier Catrice, Thomas Chertemps, Carole Couture, Laurent Deliere, Angela E. Douglas, Keith Dufault-Thompson, Paula Escuer, Honglin Feng, Astrid Forneck, Toni Gabaldon, Roderic Guigo, Frederique Hilliou, Silvia Hinojosa-Alvarez, Yi-Min Hsiao, Sylvie Hudaverdian, Emmanuelle Jacquin-Joly, Edward B. James, Spencer Johnston, Benjamin Joubard, Gaelle Le Goff, Gael Le Trionnaire, Pablo Librado, Shanlin Liu, Eric Lombaert, Hsiao-Ling Lu, Martine Maibeche, Mohamed Makni, Marina Marcet-Houben, David Martinez-Torres, Camille Meslin, Nicolas Montagne, Nancy A. Moran, Daciana Papura, Nicolas Parisot, Yvan Rahbe, Melanie Ribeiro Lopes, Aida Ripoll-Cladellas, Stephanie Robin, Celine Roques, Pascale Roux, Julio Rozas, Alejandro Sanchez-Gracia, Jose F. Sanchez-Herrero, Didac Santesmasses, Iris Scatoni, Remy-Felix Serre, Ming Tang, Wenhua Tian, Paul A. Umina, Manuella van Munster, Carole Vincent-Monegat, Joshua Wemmer, Alex C. C. Wilson, Ying Zhang, Chaoyang Zhao, Jing Zhao, Serena Zhao, Xin Zhou, Francois Delmotte, Denis Tagu
Article
Microbiology
Zachary T. Pimentel, Keith Dufault-Thompson, Kayla T. Russo, Abigail K. Scro, Roxanna M. Smolowitz, Marta Gomez-Chiarri, Ying Zhang
Summary: Marine invertebrate microbiomes, specifically in the eastern oyster Crassostrea virginica, exhibit high variability across tissue types and individual oysters. The dominant bacterial taxon in the gut of the oyster is the class Mollicutes, which shows a distinct metabolic function compared to related genomes. This study represents the first metagenomics-derived functional inference of Mollicutes in the eastern oyster microbiome.
Article
Oncology
Roma Bhuta, Bradley DeNardo, Jing Wang, Janet Atoyan, Ying Zhang, David Nelson, Jason Shapiro
Summary: Long-term changes in the gut microbiome after acute lymphoblastic leukemia therapy show significant differences in bacterial strains and diversity between pediatric ALL survivors and healthy sibling controls, lasting for years after completion of therapy.
PEDIATRIC BLOOD & CANCER
(2021)
Article
Microbiology
Dmitry A. Rodionov, Irina A. Rodionova, Vladimir A. Rodionov, Aleksandr A. Arzamasov, Ke Zhang, Gabriel M. Rubinstein, Tania N. N. Tanwee, Ryan G. Bing, James R. Crosby, Intawat Nookaew, Mirko Basen, Steven D. Brown, Charlotte M. Wilson, Dawn M. Klingeman, Farris L. Poole, Ying Zhang, Robert M. Kelly, Michael W. W. Adams
Summary: Extremely thermophilic bacteria from the genus Caldicellulosiruptor can degrade polysaccharide components of plant cell walls and subsequently utilize the constituting mono-and oligosaccharides to produce ethanol and other industrially important end products. Transcriptional regulation mechanisms of carbohydrate utilization genes were investigated using a comparative genomics approach, revealing a complex regulatory network controlling the expression of genes involved in degradation of plant biomass. The reconstruction of carbohydrate utilization regulatory network improved functional annotations of transporters and catabolic enzymes, providing insights for metabolic engineering strategies to optimize yields of bio-based fuels and chemicals from lignocellulose, with a focus on Caldicellulosiruptor bescii.
Article
Microbiology
Yunha Hwang, Dirk Schulze-Makuch, Felix L. Arens, Johan S. Saenz, Panagiotis S. Adam, Christof Sager, Till L. Bornemann, Weishu Zhao, Ying Zhang, Alessandro Airo, Michael Schloter, Alexander J. Probst
Summary: The study discovered significantly different microbial communities in soils below and beside boulders in the hyperarid core of the Atacama Desert, with highly adapted Thaumarchaeaota possessing ammonia oxidation and carbon fixation potential. Genomes of Ca. Nitrosodeserticola provide insights into a thaumarchaeal lineage found in globally distributed terrestrial habitats characterized by various environmental stresses, expanding the genetic repertoire of Thaumarchaeota and the diversity of microbiome functioning in hyperarid ecosystems.
Article
Neurosciences
Saber Meamardoost, Mahasweta Bhattacharya, Eun Jung Hwang, Takaki Komiyama, Claudia Mewes, Linbing Wang, Ying Zhang, Rudiyanto Gunawan
Summary: The study developed a MATLAB package called FARCI for inferring neuronal connectomes from high-dimensional two-photon Calcium fluorescence data, using partial correlations as a measure of functional association strength between neuron pairs. Testing on simulated datasets demonstrated that FARCI provides accurate connectomes and is robust to network sizes, missing neurons, and noise levels. Compared to other algorithms, FARCI produces more accurate networks, with better computational speed and scalability.
Article
Microbiology
Keith Dufault-Thompson, Chang Nie, Huahua Jian, Fengping Wang, Ying Zhang
Summary: Microbial acclimation to temperature conditions can lead to changes in cell composition and metabolic efficiency. This study used genome-scale models to simulate the metabolic responses of a deep-sea psychrophilic bacterium under different temperatures. The models predicted differences in metabolic efficiency and rearrangement of metabolic pathways, which were validated through comparisons to transcriptomes. This study highlights the utility of modeling approaches in studying the temperature-driven metabolic responses of extremophilic organisms.
Article
Biotechnology & Applied Microbiology
James R. Crosby, Tunyaboon Laemthong, Ryan G. Bing, Ke Zhang, Tania N. N. Tanwee, Gina L. Lipscomb, Dmitry A. Rodionov, Ying Zhang, Michael W. W. Adams, Robert M. Kelly
Summary: This study characterizes the utilization of hemicellulose by the extreme thermophile Caldicellulosiruptor bescii by integrating genomic reconstruction, transcriptomic data, operon structures, and biochemical characteristics of key enzymes. The comparative genomics of the genus also reveals conserved and divergent mechanisms for hemicellulose utilization across the 15 sequenced species. These findings are essential for understanding lignocellulose degradation and can contribute to enhancing lignocellulose conversion for biofuel and chemical production through metabolic engineering efforts.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Engineering, Biomedical
Fangyu Liu, Saber Meamardoost, Rudiyanto Gunawan, Takaki Komiyama, Claudia Mewes, Ying Zhang, EunJung Hwang, Linbing Wang
Summary: In this study, deep learning was applied to neural decoding, and the performance of different decoding schemes was evaluated. The results showed that deep learning networks outperformed traditional machine learning algorithms in some decoding schemes, indicating the potential of deep learning for behavior decoding.
JOURNAL OF NEURAL ENGINEERING
(2022)
Article
Environmental Sciences
Christopher Powers, Fatma Gomaa, Elizabeth B. Billings, Daniel R. Utter, David J. Beaudoin, Virginia P. Edgcomb, Colleen M. Hansel, Scott D. Wankel, Helena L. Filipsson, Ying Zhang, Joan M. Bernhard
Summary: This study used transcriptomics and metatranscriptomics to investigate the gene expression differences of two benthic foraminifera species thriving in oxygen-depleted marine sediments, revealing their utilization of adaptable mitochondrial and peroxisomal metabolism to adapt to varying oxygen levels and chemical environments.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Microbiology
Zachary T. Pimentel, Patricia S. Thibodeau, Bongkeun Song, Ying Zhang
Summary: This study obtained a nearly complete genome of an uncultured Mollicutes sp. from the gut metagenome of Limacina rangii, an open-ocean snail in the rapidly warming region of the western Antarctic Peninsula. The findings suggest that this species plays an important role in the ecosystem as a grazer and prey for higher trophic animals.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Biotechnology & Applied Microbiology
Gina L. Lipscomb, Alexander T. Crowley, Diep M. N. Nguyen, Matthew W. Keller, Hailey C. O'Quinn, Tania N. N. Tanwee, Jason L. Vailionis, Ke Zhang, Ying Zhang, Robert M. Kelly, Michael W. W. Adams
Summary: Scientists have engineered ethanol production at 95 degrees C by the hyperthermophilic archaeon Pyrococcus furiosus, breaking the previous highest temperature record of 85 degrees C. This study provides potential technical support for high-temperature fermentation of ethanol production and opens up new possibilities in the field of biotechnology.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Cecile M. Cres, Andrew Tritt, Kristofer E. Bouchard, Ying Zhang
Summary: DL-TODA is a program that uses a deep learning model to classify metagenomic reads, achieving high classification accuracy. It outperforms other state-of-the-art taxonomic classification tools and can be applied to analyze microbiomes from diverse environments.
Article
Microbiology
Sarah P. Esser, Janina Rahlff, Weishu Zhao, Michael Predl, Julia Plewka, Katharina Sures, Franziska Wimmer, Janey Lee, Panagiotis S. Adam, Julia McGonigle, Victoria Turzynski, Indra Banas, Katrin Schwank, Mart Krupovic, Till L. V. Bornemann, Perla Abigail Figueroa-Gonzalez, Jessica Jarett, Thomas Rattei, Yuki Amano, Ian K. Blaby, Jan-Fang Cheng, William J. Brazelton, Chase L. Beisel, Tanja Woyke, Ying Zhang, Alexander J. Probst
Summary: CRISPR spacers in DPANN archaea can target chromosomal DNA of their episymbionts, and this phenomenon is widespread across different archaeal lineages. Using metagenomics, metatranscriptomics, and single-cell genomics, researchers found that CRISPR spacers in Candidatus Altiarchaeum crystalense and Ca. A. horonobense match putative essential genes in their episymbionts' genomes. Metabolic interaction modeling also indicates that episymbionts can be either parasitic or mutualistic depending on the host genotype. Moreover, CRISPR-Cas targeting of genomes associated with symbiotic archaea is independently evolved in various archaeal lineages, as suggested by an analysis of 7,012 archaeal genomes.
NATURE MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Fatma Gomaa, Daniel R. Utter, Christopher Powers, David J. Beaudoin, Virginia P. Edgcomb, Helena L. Filipsson, Colleen M. Hansel, Scott D. Wankel, Ying Zhang, Joan M. Bernhard
Summary: This study found that some foraminifera thrive in oxygen-depleted to anoxic sediments in marine ecosystems, utilizing unique metabolic strategies and functional integration to gain an advantage, adapting to ongoing oceanic deoxygenation.
