Article
Environmental Sciences
Clara Jegousse, Pauline Vannier, Rene Groben, Kristinn Guomundsson, Viggo Thor Marteinsson
Summary: This study investigated the taxonomic and metabolic diversity of marine microorganisms in Icelandic waters using molecular techniques. The results showed correlations between microbial community profiles and water masses, as well as differences in microbial diversity related to seawater temperature. Additionally, three photosynthetic microorganisms were identified as valuable indicators for future monitoring and ecosystem modeling.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
C. McCall, H. Wu, E. O'Brien, I. Xagoraraki
Summary: This study investigated enteric viruses in wastewater during an outbreak of acute hepatitis caused by hepatitis A virus in Detroit. The research found that HAV, norovirus and sapovirus were present in untreated wastewater, with HAV loads significantly correlated with disease cases reported. The study highlights the potential of metagenomics for genogrouping and surveillance of enteric viruses.
JOURNAL OF APPLIED MICROBIOLOGY
(2021)
Review
Dentistry, Oral Surgery & Medicine
Purnima S. Kumar, Shareef M. Dabdoub, Sukirth M. Ganesan
Summary: The study of the periodontal microbial community has been influenced by a long history of cultivation-based and microscopic investigations, leading to the recognition of a discrepancy between culturable and uncultured bacteria. The development of DNA sequencing as a tool to study microbial dark matter has revolutionized the field, enabling the discovery of new species and functions and challenging traditional views on the role of the oral microbiome in health and disease.
PERIODONTOLOGY 2000
(2021)
Review
Microbiology
Karrie K. K. Ko, Kern Rei Chng, Niranjan Nagarajan
Summary: Lessons learnt from the COVID-19 pandemic emphasize the importance of awareness and surveillance for zoonoses, emerging infectious diseases, and antimicrobial resistance. Metagenomics-based surveillance methods offer a promising solution for improving early detection of pathogens.
NATURE MICROBIOLOGY
(2022)
Article
Microbiology
Kranti Konganti, Elizabeth Reed, Mark Mammel, Tunc Kayikcioglu, Rachel Binet, Karen Jarvis, Christina M. M. Ferreira, Rebecca L. L. Bell, Jie Zheng, Amanda M. M. Windsor, Andrea Ottesen, Christopher J. J. Grim, Padmini Ramachandran
Summary: Most current Salmonella subtyping analyses rely on whole genome sequencing (WGS), which focuses on the high-resolution analysis of single genomes or multiple single genomes from the isolated colonies on microbiological agar plates. In this study, bioinformatics innovations were introduced for a metagenomic outbreak response workflow that accurately identifies multiple Salmonella serovars at the same time. bettercallsal outperformed k-mer, Seqsero2, and Kallisto in identifying multiple serovars from enrichment cultures using shotgun metagenomic sequencing.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Koray Ergunay, Mathew Mutinda, Brian Bourke, Silvia A. Justi, Laura Caicedo-Quiroga, Joseph Kamau, Samson Mutura, Irene Karagi Akunda, Elizabeth Cook, Francis Gakuya, Patrick Omondi, Suzan Murray, Dawn Zimmerman, Yvonne-Marie Linton
Summary: This study focused on using ticks as xenosurveillance sentinels to detect circulating pathogens in Kenyan drylands. Host-feeding ticks collected from various wild animals and domestic animals were screened using metagenomics. The results showed that ticks carried a wide range of pathogenic bacteria, viruses, and fungi, with the potential for transmission between wildlife, livestock, and humans in the Kenyan landscape.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
David F. Nieuwenhuijse, Anne van der Linden, Robert H. G. Kohl, Reina S. Sikkema, Marion P. G. Koopmans, Bas B. Oude Munnink
Summary: This study explores the importance of genetic sequencing during outbreaks for public health decision making and compares different whole genome sequencing methods on the Nanopore and Illumina platforms. The findings suggest that the choice of sequencing approach and platform depends on the purpose of genome sequencing.
Article
Biochemistry & Molecular Biology
Chaofang Zhong, Chaoyun Chen, Lusheng Wang, Kang Ning
Summary: Advances in sequencing technology have enabled in-depth profiling of microbial communities through pan-genome and metagenome analysis. The combination of pan-genome and metagenome approaches is seen as a promising method for tracking microbial sources and deciphering population-level evolution. Advanced analytical techniques, including big-data based artificial intelligence, are expected to further enhance our understanding of microbial community patterns.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Environmental Sciences
Ajaya Kumar Rout, Budheswar Dehury, Pranaya Kumar Parida, Dhruba Jyoti Sarkar, Bhaskar Behera, Basanta Kumar Das, Anil Rai, Bijay Kumar Behera
Summary: This study investigates the structure and functions of the microbial community in the polluted sediments of the Ganga River in India using high-resolution metagenomics. Bacteria dominate the sediment samples, particularly the Pseudomonadota phylum, which is involved in the degradation of various xenobiotic compounds. Pathway analysis reveals an abundance of genes related to energy metabolism, as well as pollutant degrading enzymes. Overall, this study provides valuable insights into the bacterial diversity and dynamics in the polluted river microbiome, which can be applied in health and bioremediation.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Environmental Sciences
Xingjie Wu, Pengfei Liu, Carl-Eric Wegner, Yu Luo, Ke-Qing Xiao, Zhenling Cui, Fusuo Zhang, Werner Liesack, Jingjing Peng
Summary: The study shows that organic material amendments significantly influence the link between microbial life history strategies and soil organic carbon storage, with a one-time peat-vermiculite application notably increasing organic carbon storage efficiency.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Microbiology
Yunha Hwang, Janina Rahlff, Dirk Schulze-Makuch, Michael Schloter, Alexander J. Probst
Summary: Viruses in Atacama Desert soils play essential roles in host-virus interactions, spreading stress resilience and metabolic genes to ensure host survival; the virus-host interactions are dynamic and complex, shaping uniquely adapted microbiomes in this highly selective and hostile environment.
Article
Infectious Diseases
Alexander W. Gofton, Kim R. Blasdell, Casey Taylor, Peter B. Banks, Michelle Michie, Emilie Roy-Dufresne, Jacqueline Poldy, Jian Wang, Michael Dunn, Mary Tachedjian, Ina Smith
Summary: Tick-borne zoonoses are emerging globally due to changes in climate and land use. In Australia, the diversity of potentially zoonotic agents carried by ticks and their significance to human and animal health is not well understood. In this study, metatranscriptomics was used to analyze tick and wildlife blood samples in New South Wales, Australia, revealing a wide range of tick-borne microorganisms, including novel putative species. These findings highlight the unique and endemic microbial fauna harbored by Australian ticks and the need for further research on their potential risks to human and animal health.
TRANSBOUNDARY AND EMERGING DISEASES
(2022)
Article
Biology
Francesco Beghini, Lauren J. McIver, Aitor Blanco-Miguez, Leonard Dubois, Francesco Asnicar, Sagun Maharjan, Ana Mailyan, Paolo Manghi, Matthias Scholz, Andrew Maltez Thomas, Mireia Valles-Colomer, George Weingart, Yancong Zhang, Moreno Zolfo, Curtis Huttenhower, Eric A. Franzosa, Nicola Segata
Summary: Culture-independent analyses of microbial communities have advanced significantly in the past decade, particularly due to the emergence of Shotgun Metagenomics. bioBakery 3, a newly developed toolset, enhances the accuracy and scope of taxonomic, functional, and phylogenetic profiling in microbial community studies by providing an expanding set of reference sequences.
Article
Microbiology
Paula Maza-Marquez, Michael D. Lee, Brad M. Bebout
Summary: The study evaluated the abundance and diversity of fungi in a hypersaline microbial mat from Guerrero Negro, Mexico, using qPCR and metagenomic sequencing. The findings revealed a rich fungal community structure with functions including saprotrophic, parasitic, and denitrification activities.
Article
Environmental Sciences
Maria R. Martinez-Gallardo, Maria J. Lopez, Juan A. Lopez-Gonzalez, Macarena M. Jurado, Francisca Suarez-Estrella, Maria D. Perez-Murcia, Jose A. Saez, Raul Moral, Joaquin Moreno
Summary: This study compares the characteristics of long-time stored OMW sludges in evaporation ponds and assesses their impact on the underlying soil layer. The results show that organic matter and toxicity levels play a significant role in affecting the microbial community, and higher toxicity and biomass carbon levels on the surface suggest reduced leach flow and depletion of contaminants. Biostimulation of natural microbiota through sustainable biological treatments could promote the bioremediation of OMW sludges, offering a potential solution to environmental concerns in olive oil-producing countries.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2021)
Article
Agronomy
Shuwei Chang, Guoqiang Huang, Duoxiang Wang, Wanwan Zhu, Jianxin Shi, Litao Yang, Wanqi Liang, Qi Xie, Dabing Zhang
Summary: This study identifies six rice SIAH-type E3 ligases and reveals their regulatory role in determining the stability of formin proteins. The study also highlights the redundancy between these six genes and provides insights into the importance of these genes in plant growth and development.
Article
Biology
Krishnendu Mukherjee, Ulrich Dobrindt
Summary: This article reviews the contributions of chromatin remodeling to insect immunity and adaptation to pathogens, focusing on the roles of DNA methylation, histone acetylation, and microRNAs in the evolution of insect resistance.
CURRENT OPINION IN INSECT SCIENCE
(2022)
Article
Evolutionary Biology
Nicolas C. H. Schroeder, Ana Korsa, Haleluya Wami, Olena Mantel, Ulrich Dobrindt, Joachim Kurtz
Summary: This study investigated the persistence and evolution of the probiotic Escherichia coli strain Nissle 1917 in an insect host and flour environment through experimental evolution. The findings suggest that EcN remains stable with weak phenotypic changes during serial passage in the insect host, indicating a certain degree of phenotypic plasticity.
EVOLUTION MEDICINE AND PUBLIC HEALTH
(2022)
Article
Plant Sciences
Jihyun Kim, Jeniffer Silva, Chanwoo Park, Younghun Kim, Nayeon Park, Johan Sukweenadhi, Junping Yu, Jianxin Shi, Dabing Zhang, Keun Ki Kim, Hong-Joo Son, Hyeon Cheal Park, Chang-Oh Hong, Kwang Min Lee, Yu-Jin Kim
Summary: Cytochrome P450 (CYP) catalyzes monooxygenation reactions in plant metabolism, with CYP703 playing a key role in fatty acid hydroxylation in male reproductive tissues. PgCYP703A4 in Korean ginseng is conserved in function, affecting fruit size and cutin synthesis through fatty acid hydroxylation pathways.
Article
Plant Sciences
Gaodian Shen, Wenli Sun, Zican Chen, Lei Shi, Jun Hong, Jianxin Shi
Summary: This review summarizes the roles of plant GELPs in regulating plant development and plant-environment interactions, as well as the potential regulatory mechanisms.
Article
Toxicology
Robert Landsiedel, Daniela Hahn, Rainer Ossig, Sabrina Ritz, Lydia Sauer, Roland Buesen, Sascha Rehm, Wendel Wohlleben, Sibylle Groeters, Volker Strauss, Saskia Sperber, Haleluya Wami, Ulrich Dobrindt, Karola Prior, Dag Harmsen, Bennard van Ravenzwaay, Juergen Schnekenburger
Summary: The analysis of intestinal microbiome and plasma metabolome can serve as an early and sensitive indicator of gut microbiome changes induced by orally administered nanoparticles; this will help to recognize potential adverse effects of these changes to the host.
PARTICLE AND FIBRE TOXICOLOGY
(2022)
Article
Plant Sciences
Jun Hong, Leah Rosental, Yang Xu, Dawei Xu, Isabel Orf, Wengsheng Wang, Zhiqiang Hu, Su Su, Shaoxing Bai, Mohammed Ashraf, Chaoyang Hu, Changquan Zhang, Zhikang Li, Jianlong Xu, Qiaoquan Liu, Hui Zhang, Fengli Zhang, Zhijing Luo, Mingjiao Chen, Xiaofei Chen, Natalie Betts, Alisdair Fernie, Wanqi Liang, Guanqun Chen, Yariv Brotman, Dabing Zhang, Jianxin Shi
Summary: This study revealed the genetic regulation of rice seed glycerolipids using metabolite-based approaches. Two genes were found to be involved in the variation of saturated triacylglycerol and lyso-phosphatidylcholine contents. The study also demonstrated the association of these genes with other traits such as heading date and flooding tolerance. The findings suggest that the diversity of rice seed glycerolipids may have been unintentionally shaped during natural and artificial selection.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Immunology
Paulo A. Schueroff, Cecilia M. Abe, Jonatas W. Silva, Cideli de Paula Coelho, Fernanda B. Andrade, Rodrigo T. Hernandes, Ulrich Dobrindt, Tania A. T. Gomes, Waldir P. Elias
Summary: This study evaluated the involvement of AFP and other adhesins in the uropathogenicity and intestinal colonization of bacteria. The results showed a synergistic role of AFP and TIF in the adherence and colonization of intestinal and urinary epithelia.
Article
Microbiology
Lang Peng, Rexford Mawunyo Dumevi, Marco Chitto, Nadja Haarmann, Petya Berger, Gerald Koudelka, Herbert Schmidt, Alexander Mellmann, Ulrich Dobrindt, Michael Berger
Summary: This study proposes a new method for genetic manipulation of enterohemorrhagic Escherichia coli (EHEC) that is more efficient than traditional methods. The method increases recombineering efficiency by 3-4 times in EHEC O157:H7 EDL933 Delta stx1/2, but shows similar efficiency in Escherichia coli K-12 MG1655. Additionally, the study suggests that the inhibition of the RecFOR pathway indirectly blocks phage induction and improves recombineering efficiency.
Article
Plant Sciences
Jun Hong, Su Su, Li Wang, Shaoxing Bai, Jianlong Xu, Zhikang Li, Natalie Betts, Wanqi Liang, Wensheng Wang, Jianxin Shi, Dabing Zhang
Summary: Plant height in rice is an important trait, and this study identified multiple genes and genetic interactions involved in regulating this trait. The discovery of a structural variant in the SD1 gene and the identification of additional genes provide valuable resources for breeding semi-dwarf rice. These findings also contribute to our understanding of the genetic mechanisms underlying plant height regulation in rice.
PLANT CELL AND ENVIRONMENT
(2023)
Review
Plant Sciences
Jianxin Shi, Gynheung An, Andreas P. M. Weber, Dabing Zhang
Summary: To achieve the goals of the UN's 2030 Agenda for Sustainable Development, transformative change is needed in our agrifood systems to ensure food security in the face of climate change, population growth, urbanization, and natural resource depletion. Rice, a major staple cereal crop, has historically contributed to global food security and will continue to do so in the future. Advances in research and breeding practices have helped meet increasing demands, but the future of rice production depends on resilient cultivars that can adapt to changing environmental conditions. This Special Issue highlights the field of rice-environment interactions and proposes future directions for rice research, including the development of environment-resilient rice varieties.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Plant Sciences
Weihua Li, Duoxiang Wang, Xiaokun Hong, Jin Shi, Jun Hong, Su Su, Cristopher Reyes Loaiciga, Jing Li, Wanqi Liang, Jianxin Shi, Dabing Zhang
Summary: Identification and validation of ten new MADS-box homologous genes in 3010 rice pan-genome for rice breeding. These genes encode transcription factors that play essential roles in rice growth and development. The discovery of these genes in the rice pan-genome provides valuable genetic resources for rice improvement, overcoming the limitation of the existing identified MADS-box genes. The expression analysis confirms their presence in flower tissues and suggests their potential roles in seed development.
PLANT CELL REPORTS
(2023)
Article
Biotechnology & Applied Microbiology
Zican Chen, Weronika Jasinska, Muhammad Ashraf, Leah Rosental, Jung Hong, Dabing Zhang, Yariv Brotman, Jianxin Shi
Summary: Arabidopsis sepals coordinate flower opening in the morning as ambient temperature rises, but the underlying molecular mechanisms are poorly understood. This study explored the role of lipids in this process by comparing lipidomic changes in sepals of mutant plants under normal and mild heat stress temperatures. The findings revealed the impact of mild heat stress on sepal lipidome and the differential effects of HSP70-16 and VDAC3 on sepal lipidomic responses.
Article
Veterinary Sciences
Inger Helene Kravik, Hakon Kaspersen, Siri Kulberg Sjurseth, Katharine Rose Dean, Bruce David, Marina Aspholm, Camilla Sekse
Summary: Avian pathogenic Escherichia coli (APEC) is a major cause of colibacillosis outbreaks in poultry chicks, resulting in high mortality and poor animal welfare. This study performed whole genome sequencing and bioinformatic analyses on 219 APEC isolates from colibacillosis broiler flocks in Norway during 2018-2021. The results revealed the prevalence of specific sequence types (STs) and identified two distinct outbreaks caused by ST429 and ST23. Additionally, combining serotyping and sequence typing was found to be useful in discriminating APEC strains.
VETERINARY RESEARCH
(2023)
Review
Plant Sciences
Yueya Zhang, Chaoqun Shen, Jin Shi, Jianxin Shi, Dabing Zhang
Summary: One of the challenges for global food security is to improve the grain yield of cereal crops by modifying their inflorescence architecture. Recent advancements in understanding the genetic regulation of inflorescence architecture in crops like rice, maize, wheat, and barley have provided valuable insights. This knowledge can be utilized to optimize inflorescence architecture and ultimately enhance crop grain yield.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)