Designer cellulosomes – catalytic nanomachines with significant potential in biotechnology and circular economy by Maša Vodovnik

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Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data by Caitlin Guccione, Lucas Patel, Yoshihiko Tomofuji, Daniel McDonald, Antonio Gonzalez, Gregory D. Sepich-Poore, Kyuto Sonehara, Mohsen Zakeri, Yang Chen, Amanda Hazel Dilmore, Neil Damle, Sergio E. Baranzini, George Hightower, Teruaki Nakatsuji, Richard L. Gallo, Ben Langmead, Yukinori Okada, Kit Curtius, Rob Knight

“…Overall, we demonstrate that rigorous host filtration is a key component of privacy-minded analyses of patient microbiomes and provide computationally efficient pipelines for accomplishing this task on large-scale datasets.…”
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Impact of a block structure on the Lotka-Volterra model by Clenet, Maxime, Massol, François, Najim, Jamal

“…The Lotka-Volterra (LV) model is a simple, robust, and versatile model used to describe large interacting systems such as food webs or microbiomes. The model consists of n coupled differential equations linking the abundances of n different species. …”
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Representative Metagenomes of Mesophilic Biogas Reactor Across South Korea by Darsha Prabhaharan, Young Wook Go, Hyunjin Kim, Seongcheol Kang, Byoung-In Sang

“…Over the past decade, this has driven global research on biogas-producing microbiomes, leading to significant advances in our understanding of microbial diversity and metabolic pathways within AD plants. …”
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Probiotics, Prebiotics, and Synbiotics: Gut and Beyond by Usha Vyas, Natarajan Ranganathan

“…Restoration of the gut microbiota may be difficult to accomplish, but the use of probiotics has led to promising results in a large number of well-designed (clinical) studies. Microbiomics has spurred a dramatic increase in scientific, industrial, and public interest in probiotics and prebiotics as possible agents for gut microbiota management and control. …”
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Biomarkers of inflammation and colorectal cancer risk by Yuting Li, Yuting Li, Yuting Li, Yuexin Luo, Yue Ran, Furong Lu, You Qin

“…Multi-omics techniques, including genomics and microbiomics, offer new avenues for CRC diagnosis. Overall, while evidence highlights the significance of inflammatory biomarkers in CRC risk prediction, larger prospective studies are urgently needed to clarify their roles due to existing inconsistencies and methodological limitations.…”
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Hologenomic data generation and analysis in wild vertebrates by Carlotta Pietroni, Nanna Gaun, Aoife Leonard, Jonas Lauritsen, Garazi Martin‐Bideguren, Iñaki Odriozola, Ostaizka Aizpurua, Antton Alberdi, Raphael Eisenhofer

“…Our results show that faecal samples are significantly better than anal and cloacal swabs to study intestinal microbiomes using genome‐resolved metagenomics. We also report that birds and bats both have substantially lower microbial DNA fractions and a higher degree of sample‐to‐sample variability compared to amphibians, reptiles and non‐flying mammals. …”
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Soil bacterial communities in urban deciduous forests are filtered by site identity, soil chemistry, and shrub presence by Derek Griffin Wu, Vincent D’Amico, Tara Lynn Eckard Trammell

“…Phylum level bacterial communities were more uniform under shrub cover versus no cover, indicative of a generalized plant effect shaping soil microbiomes. Correlations between bacterial phyla and soil chemistry varied, with some phyla positively or negatively correlating with the same property at different sites. …”
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A single vector system for tunable and homogeneous dual gene expression in Escherichia coli by Z. Živič, L. Lipoglavšek, J. Lah, S. Hadži

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Ecological drift during colonization drives within-host and between-host heterogeneity in an animal-associated symbiont. by Jason Z Chen, Zeeyong Kwong, Nicole M Gerardo, Nic M Vega

“…Our findings illuminate the processes that might affect symbiont transmission, coinfection, and population structure in nature, which can drive the evolution of host-microbe symbioses and microbe-microbe interactions within host-associated microbiomes.…”
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An atlas of metabolites driving chemotaxis in prokaryotes by Maéva Brunet, Shady A. Amin, Iurii Bodachivskyi, Unnikrishnan Kuzhiumparambil, Justin R. Seymour, Jean-Baptiste Raina

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Unveiling the mechanism of micro-and-nano plastic phytotoxicity on terrestrial plants: A comprehensive review of omics approaches by Asad Jamil, Ambreen Ahmad, Muhammad Moeen-ud-din, Yihao Zhang, Yuxuan Zhao, Xiaochen Chen, Xiaoyu Cui, Yindong Tong, Xianhua Liu

“…Recent advancements in omics technologies such as proteomics, metabolomics, transcriptomics, and microbiomics, coupled with emerging technologies like 4D omics, phenomics, spatial transcriptomics, and single-cell omics, offer unprecedented insight into the physiological, molecular, and cellular responses of terrestrial plants to MNPs exposure. …”
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Antibacterial and antioxidant potentials, detection of host origin compounds, and metabolic profiling of endophytic Bacillus spp. isolated from Rauvolfia serpentina (L.) Benth. ex... by Rusi Lata, Surendra Kumar Gond

“…Abstract The research highlights the importance of exploring endophytic microbiomes of medicinal plants to uncover their potential for secondary metabolite production and their role in the biosynthesis of host-derived compounds. …”
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Responses of fungal communities at different soil depths to grazing intensity in a desert steppe by Xiangjian Tu, Paul C. Struik, Shixian Sun, Zhang Wenbo, Yong Zhang, Ke Jin, Zhen Wang

“…This provides empirical support for coping with the impact of grazing on soil microbiomes in desert steppes.…”
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Contaminant-degrading bacteria are super carriers of antibiotic resistance genes in municipal landfills: A metagenomics-based study by Fang-Zhou Gao, Wei-Li Jia, Bing Li, Min Zhang, Liang-Ying He, Hong Bai, You-Sheng Liu, Guang-Guo Ying

“…Klebsiella pneumoniae, Acinetobacter nosocomialis and Escherichia coli were abundant multidrug-resistant pathogenic species in raw leachate (∼10.2 % of total microbiomes), but they rarely carried contaminant-degradation genes. …”
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Predictive, preventive and personalized project of vascular cognitive impairment in China (P3): Study design and interim baseline patient characteristics of a Nationwide multicente... by Linlin Wang, Jiwei Jiang, Yanli Wang, Gaifen Liu, Wenyi Li, Qiwei Ren, Shirui Jiang, Min Zhao, Huiying Zhang, Tianlin Jiang, Shiyi Yang, Mei Cui, Qiang Dong, Jun Xu

“…Through multidimensional analysis of clinical information, radiomics, proteomics, metabolomics, microbiomics, and genetics, provide a more comprehensive understanding of VCI trajectories and individual variability, enhancing early detection and prognosis management.…”
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Using genomics to explore the epidemiology of vancomycin resistance in a sewage system by Emilie Egholm Bruun Jensen, Saria Otani, Ivan Liachko, Benjamin Auch, Frank M. Aarestrup

“…Our results also suggest that over the +20 years of colonizing a sewer system, vanHAX has not become widespread across multiple taxa, remaining primarily in E. faecalis and E. faecium, with the exception of Paenibacillus.IMPORTANCELong-term colonization of microbial communities with antimicrobial-resistant bacteria is expected to result in sharing of the resistance genes between several different bacterial taxa of the communities. We investigated microbiomes from a sewer, which have been colonized with glycopeptide-resistant bacteria harboring the mobile vanHAX gene cluster for a minimum of 20 years, using metagenomics sequencing and Hi-C. …”
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ITS amplicon sequencing revealed that rare taxa of tea rhizosphere fungi are closely related to the environment and provide feedback on tea tree diseases by Yuanqi Zhao, Weiwei Ran, Wenming Xu, Yuehua Song

“…Our aim is to offer insights for the advancement of modern agriculture in ecologically fragile karst tea gardens, as well as microbiomics concepts for green and sustainable environmental development. …”
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Immunological composition of human milk before and during subclinical and clinical mastitis by Irma Castro-Navarro, Ryan M. Pace, Ryan M. Pace, Ryan M. Pace, Janet E. Williams, Christina D. W. Pace, Harpreet Kaur, Julia Piaskowski, Alberto Aragón, Alberto Aragón, Juan M. Rodríguez, Juan M. Rodríguez, Mark A. McGuire, Leonides Fernandez, Leonides Fernandez, Michelle K. McGuire

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Sdd3 regulates the biofilm formation of Candida albicans via the Rho1-PKC-MAPK pathway by Li Mei Pang, Guisheng Zeng, Eve Wai Ling Chow, Xiaoli Xu, Ning Li, Yee Jiun Kok, Shu Chen Chong, Xuezhi Bi, Jiaxin Gao, Chaminda Jayampath Seneviratne, Yue Wang

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