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Lose-lose consequences of bacterial community-driven invasions in soil Microbiome (IF 15.5) Pub Date : 2024-03-18 Xipeng Liu, Joana Falcão Salles
Community-driven invasion, also known as community coalescence, occurs widely in natural ecosystems. Despite that, our knowledge about the process and mechanisms controlling community-driven invasion in soil ecosystems is lacking. Here, we performed a set of coalescence experiments in soil microcosms and assessed impacts up to 60 days after coalescence by quantifying multiple traits (compositional
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Intact lung tissue and bronchoalveolar lavage fluid are both suitable for the evaluation of murine lung microbiome in acute lung injury Microbiome (IF 15.5) Pub Date : 2024-03-18 Lijun Zheng, Chengjun Liu, Hongjing Wang, Jun Zhang, Lejiao Mao, Xiaomei Dong, Siyao Hu, Na Li, Dandan Pi, Jingfu Qiu, Feng Xu, Chengzhi Chen, Zhen Zou
Accumulating clinical evidence suggests that lung microbiome is closely linked to the progression of pulmonary diseases; however, it is still controversial which specimen type is preferred for the evaluation of lung microbiome. To address this issue, we established a classical acute lung injury (ALI) mice model by intratracheal instillation of lipopolysaccharides (LPS). We found that the bacterial
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Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants Microbiome (IF 15.5) Pub Date : 2024-03-16 Huifeng Hu, Jannie Munk Kristensen, Craig William Herbold, Petra Pjevac, Katharina Kitzinger, Bela Hausmann, Morten Kam Dahl Dueholm, Per Halkjaer Nielsen, Michael Wagner
Microorganisms are responsible for nutrient removal and resource recovery in wastewater treatment plants (WWTPs), and their diversity is often studied by 16S rRNA gene amplicon sequencing. However, this approach underestimates the abundance and diversity of Patescibacteria due to the low coverage of commonly used PCR primers for this highly divergent bacterial phylum. Therefore, our current understanding
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Global prevalence of organohalide-respiring bacteria dechlorinating polychlorinated biphenyls in sewage sludge Microbiome (IF 15.5) Pub Date : 2024-03-16 Guofang Xu, Siyan Zhao, Matthew J. Rogers, Chen Chen, Jianzhong He
Massive amounts of sewage sludge are generated during biological sewage treatment and are commonly subjected to anaerobic digestion, land application, and landfill disposal. Concurrently, persistent organic pollutants (POPs) are frequently found in sludge treatment and disposal systems, posing significant risks to both human health and wildlife. Metabolically versatile microorganisms originating from
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A first characterization of the microbiota-resilience link in swine Microbiome (IF 15.5) Pub Date : 2024-03-15 Enrico Mancin, Christian Maltecca, Yi Jian Huang, Roberto Mantovani, Francesco Tiezzi
The gut microbiome plays a crucial role in understanding complex biological mechanisms, including host resilience to stressors. Investigating the microbiota-resilience link in animals and plants holds relevance in addressing challenges like adaptation of agricultural species to a warming environment. This study aims to characterize the microbiota-resilience connection in swine. As resilience is not
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Mapping the widespread distribution and transmission dynamics of linezolid resistance in humans, animals, and the environment Microbiome (IF 15.5) Pub Date : 2024-03-13 Weiyi Shen, Chang Cai, Ning Dong, Jiawei Chen, Rong Zhang, Jiachang Cai
The rise of linezolid resistance has been widely observed both in clinical and non-clinical settings. However, there were still data gaps regarding the comprehensive prevalence and interconnections of linezolid resistance genes across various niches. We screened for potential linezolid resistance gene reservoirs in the intestines of both humans and animals, in meat samples, as well as in water sources
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Biofilm colonization and succession in a full-scale partial nitritation-anammox moving bed biofilm reactor Microbiome (IF 15.5) Pub Date : 2024-03-12 Carolina Suarez, Tage Rosenqvist, Ivelina Dimitrova, Christopher J. Sedlacek, Oskar Modin, Catherine J. Paul, Malte Hermansson, Frank Persson
Partial nitritation-anammox (PNA) is a biological nitrogen removal process commonly used in wastewater treatment plants for the treatment of warm and nitrogen-rich sludge liquor from anaerobic digestion, often referred to as sidestream wastewater. In these systems, biofilms are frequently used to retain biomass with aerobic ammonia-oxidizing bacteria (AOB) and anammox bacteria, which together convert
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Perturbation and resilience of the gut microbiome up to 3 months after β-lactams exposure in healthy volunteers suggest an important role of microbial β-lactamases Microbiome (IF 15.5) Pub Date : 2024-03-12 Camille d’Humières, Margot Delavy, Laurie Alla, Farid Ichou, Emilie Gauliard, Amine Ghozlane, Florence Levenez, Nathalie Galleron, Benoit Quinquis, Nicolas Pons, Jimmy Mullaert, Antoine Bridier-Nahmias, Bénédicte Condamine, Marie Touchon, Dominique Rainteau, Antonin Lamazière, Philippe Lesnik, Maharajah Ponnaiah, Marie Lhomme, Natacha Sertour, Savannah Devente, Jean-Denis Docquier, Marie-Elisabeth
Antibiotics notoriously perturb the gut microbiota. We treated healthy volunteers either with cefotaxime or ceftriaxone for 3 days, and collected in each subject 12 faecal samples up to day 90. Using untargeted and targeted phenotypic and genotypic approaches, we studied the changes in the bacterial, phage and fungal components of the microbiota as well as the metabolome and the β-lactamase activity
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Interindividual differences in aronia juice tolerability linked to gut microbiome and metabolome changes—secondary analysis of a randomized placebo-controlled parallel intervention trial Microbiome (IF 15.5) Pub Date : 2024-03-09 Sonja Lackner, Alexander Mahnert, Christine Moissl-Eichinger, Tobias Madl, Hansjörg Habisch, Nathalie Meier-Allard, Christina Kumpitsch, Theresa Lahousen, Alexandra Kohlhammer-Dohr, Sabrina Mörkl, Herbert Strobl, Sandra Holasek
Aronia melanocarpa is a berry rich in polyphenols known for health benefits. However, the bioavailability of polyphenols has been questioned, and the individual taste acceptance of the fruit with its specific flavor varies. We recently observed substantial differences in the tolerability of aronia juice among healthy females, with half of the individuals tolerating aronia juice without complaints.
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Multi-omics reveals that alkaline mineral water improves the respiratory health and growth performance of transported calves Microbiome (IF 15.5) Pub Date : 2024-03-08 Jiancheng Qi, Linli Gan, Fangyuan Huang, Yue Xie, Hongrui Guo, Hengmin Cui, Junliang Deng, Liping Gou, Dongjie Cai, Chunhui Pan, Xia Lu, Ali Mujtaba Shah, Jing Fang, Zhicai Zuo
Long-distance transportation, a frequent practice in the cattle industry, stresses calves and results in morbidity, mortality, and growth suppression, leading to welfare concerns and economic losses. Alkaline mineral water (AMW) is an electrolyte additive containing multiple mineral elements and shows stress-mitigating effects on humans and bovines. Here, we monitored the respiratory health status
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Macroalgal microbiomes unveil a valuable genetic resource for halogen metabolism Microbiome (IF 15.5) Pub Date : 2024-03-07 Anna Lavecchia, Bruno Fosso, Aschwin H. Engelen, Sara Borin, Caterina Manzari, Ernesto Picardi, Graziano Pesole, Antonio Placido
Macroalgae, especially reds (Rhodophyta Division) and browns (Phaeophyta Division), are known for producing various halogenated compounds. Yet, the reasons underlying their production and the fate of these metabolites remain largely unknown. Some theories suggest their potential antimicrobial activity and involvement in interactions between macroalgae and prokaryotes. However, detailed investigations
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The astounding exhaustiveness and speed of the Astral mass analyzer for highly complex samples is a quantum leap in the functional analysis of microbiomes Microbiome (IF 15.5) Pub Date : 2024-03-07 Thibaut Dumas, Roxana Martinez Pinna, Clément Lozano, Sonja Radau, Olivier Pible, Lucia Grenga, Jean Armengaud
By analyzing the proteins which are the workhorses of biological systems, metaproteomics allows us to list the taxa present in any microbiota, monitor their relative biomass, and characterize the functioning of complex biological systems. Here, we present a new strategy for rapidly determining the microbial community structure of a given sample and designing a customized protein sequence database to
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Proportion-based normalizations outperform compositional data transformations in machine learning applications Microbiome (IF 15.5) Pub Date : 2024-03-05 Aaron Yerke, Daisy Fry Brumit, Anthony A. Fodor
Normalization, as a pre-processing step, can significantly affect the resolution of machine learning analysis for microbiome studies. There are countless options for normalization scheme selection. In this study, we examined compositionally aware algorithms including the additive log ratio (alr), the centered log ratio (clr), and a recent evolution of the isometric log ratio (ilr) in the form of balance
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Host genotype-specific rhizosphere fungus enhances drought resistance in wheat Microbiome (IF 15.5) Pub Date : 2024-03-04 Hong Yue, Xuming Sun, Tingting Wang, Ali Zhang, Dejun Han, Gehong Wei, Weining Song, Duntao Shu
The severity and frequency of drought are expected to increase substantially in the coming century and dramatically reduce crop yields. Manipulation of rhizosphere microbiomes is an emerging strategy for mitigating drought stress in agroecosystems. However, little is known about the mechanisms underlying how drought-resistant plant recruitment of specific rhizosphere fungi enhances drought adaptation
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New insights into bioaugmented removal of sulfamethoxazole in sediment microcosms: degradation efficiency, ecological risk and microbial mechanisms Microbiome (IF 15.5) Pub Date : 2024-02-29 Jianfei Chen, Xiuli Chen, Ying Zhu, Shuang Yan, Shuguang Xie
Bioaugmentation has the potential to enhance the ability of ecological technology to treat sulfonamide-containing wastewater, but the low viability of the exogenous degraders limits their practical application. Understanding the mechanism is important to enhance and optimize performance of the bioaugmentation, which requires a multifaceted analysis of the microbial communities. Here, DNA-stable isotope
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Host starvation and in hospite degradation of algal symbionts shape the heat stress response of the Cassiopea-Symbiodiniaceae symbiosis Microbiome (IF 15.5) Pub Date : 2024-02-29 Gaëlle Toullec, Nils Rädecker, Claudia Pogoreutz, Guilhem Banc-Prandi, Stéphane Escrig, Christel Genoud, Cristina Martin Olmos, Jorge Spangenberg, Anders Meibom
Global warming is causing large-scale disruption of cnidarian-Symbiodiniaceae symbioses fundamental to major marine ecosystems, such as coral reefs. However, the mechanisms by which heat stress perturbs these symbiotic partnerships remain poorly understood. In this context, the upside-down jellyfish Cassiopea has emerged as a powerful experimental model system. We combined a controlled heat stress
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Bacteroides salyersiae is a potent chondroitin sulfate-degrading species in the human gut microbiota Microbiome (IF 15.5) Pub Date : 2024-02-29 Yamin Wang, Mingfeng Ma, Wei Dai, Qingsen Shang, Guangli Yu
Chondroitin sulfate (CS) has widely been used as a symptomatic slow-acting drug or a dietary supplement for the treatment and prevention of osteoarthritis. However, CS could not be absorbed after oral intake due to its polyanionic nature and large molecular weight. Gut microbiota has recently been proposed to play a pivotal role in the metabolism of drugs and nutrients. Nonetheless, how CS is degraded
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From phyllosphere to insect cuticles: silkworms gather antifungal bacteria from mulberry leaves to battle fungal parasite attacks Microbiome (IF 15.5) Pub Date : 2024-02-26 Pengfei Zhao, Song Hong, Yuekun Li, Haimin Chen, Hanchun Gao, Chengshu Wang
Bacterial transfers from plants to insect herbivore guts have been well investigated. However, bacterial exchanges between plant phyllospheres and insect cuticles remain unclear, as does their related biological function. Here, we report that the cuticular bacterial loads of silkworm larvae quickly increased after molting and feeding on the white mulberry (Morus alba) leaves. The isolation and examination
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Time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies predominates the methanogen dynamics in Philippine rice field soil Microbiome (IF 15.5) Pub Date : 2024-02-26 Xin Li, Qicheng Bei, Mehrdad Rabiei Nematabad, Jingjing Peng, Werner Liesack
The final step in the anaerobic decomposition of biopolymers is methanogenesis. Rice field soils are a major anthropogenic source of methane, with straw commonly used as a fertilizer in rice farming. Here, we aimed to decipher the structural and functional responses of the methanogenic community to rice straw addition during an extended anoxic incubation (120 days) of Philippine paddy soil. The research
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Multi-omics reveal mechanisms of high enteral starch diet mediated colonic dysbiosis via microbiome-host interactions in young ruminant Microbiome (IF 15.5) Pub Date : 2024-02-24 Chunjia Jin, Shengru Wu, Ziqi Liang, Jun Zhang, Xinjian Lei, Hanxun Bai, Gaofeng Liang, Xiaodong Su, Xiaodong Chen, Peiyue Wang, Yue Wang, Leluo Guan, Junhu Yao
Although rumen development is crucial, hindgut undertakes a significant role in young ruminants’ physiological development. High-starch diet is usually used to accelerate rumen development for young ruminants, but always leading to the enteral starch overload and hindgut dysbiosis. However, the mechanism behind remains unclear. The combination of colonic transcriptome, colonic luminal metabolome, and
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Gut microbiota modulation enhances the immune capacity of lizards under climate warming Microbiome (IF 15.5) Pub Date : 2024-02-22 Jing Yang, Weiqiang Liu, Xingzhi Han, Xin Hao, Qibin Yao, Weiguo Du
Host-microbial interactions are expected to affect species’ adaptability to climate change but have rarely been explored in ectothermic animals. Some studies have shown that short-term warming reduced gut microbial diversity that could hamper host functional performance. However, our longitudinal experiments in semi-natural conditions demonstrated that warming decreased gut microbiota diversity at
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Novel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics Microbiome (IF 15.5) Pub Date : 2024-02-22 Lauren F. Messer, Charlotte E. Lee, Ruddy Wattiez, Sabine Matallana-Surget
Microbial functioning on marine plastic surfaces has been poorly documented, especially within cold climates where temperature likely impacts microbial activity and the presence of hydrocarbonoclastic microorganisms. To date, only two studies have used metaproteomics to unravel microbial genotype–phenotype linkages in the marine ‘plastisphere’, and these have revealed the dominance of photosynthetic
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Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging Microbiome (IF 15.5) Pub Date : 2024-02-22 Shalini Singh, Leila B. Giron, Maliha W. Shaikh, Shivanjali Shankaran, Phillip A. Engen, Zlata R. Bogin, Simona A. Bambi, Aaron R. Goldman, Joao L. L. C. Azevedo, Lorena Orgaz, Nuria de Pedro, Patricia González, Martin Giera, Aswin Verhoeven, Elena Sánchez-López, Ivona Pandrea, Toshitha Kannan, Ceylan E. Tanes, Kyle Bittinger, Alan L. Landay, Michael J. Corley, Ali Keshavarzian, Mohamed Abdel-Mohsen
People living with HIV (PLWH), even when viral replication is controlled through antiretroviral therapy (ART), experience persistent inflammation. This inflammation is partly attributed to intestinal microbial dysbiosis and translocation, which may lead to non-AIDS-related aging-associated comorbidities. The extent to which living with HIV — influenced by the infection itself, ART usage, sexual orientation
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Virome diversity shaped by genetic evolution and ecological landscape of Haemaphysalis longicornis Microbiome (IF 15.5) Pub Date : 2024-02-21 Run-Ze Ye, Yu-Yu Li, Da-Li Xu, Bai-Hui Wang, Xiao-Yang Wang, Ming-Zhu Zhang, Ning Wang, Wan-Ying Gao, Cheng Li, Xiao-Yu Han, Li-Feng Du, Luo-Yuan Xia, Ke Song, Qing Xu, Jing Liu, Nuo Cheng, Ze-Hui Li, Yi-Di Du, Hui-Jun Yu, Xiao-Yu Shi, Jia-Fu Jiang, Yi Sun, Xiao-Ming Cui, Shu-Jun Ding, Lin Zhao, Wu-Chun Cao
Haemaphysalis longicornis is drawing attentions for its geographic invasion, extending population, and emerging disease threat. However, there are still substantial gaps in our knowledge of viral composition in relation to genetic diversity of H. longicornis and ecological factors, which are important for us to understand interactions between virus and vector, as well as between vector and ecological
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Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3 Microbiome (IF 15.5) Pub Date : 2024-02-20 Wenzhi Hao, Qingyu Ma, Lu Wang, Naijun Yuan, Hua Gan, Liangliang He, Xiaojuan Li, Junqing Huang, Jiaxu Chen
Remodeling eubiosis of the gut microenvironment may contribute to preventing the occurrence and development of depression. Mounting experimental evidence has shown that complement C3 signaling is associated with the pathogenesis of depression, and disruption of the gut microbiota may be an underlying cause of complement system activation. However, the mechanism by which complement C3 participates in
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Integrated meta-omics reveals the regulatory landscape involved in lipid metabolism between pig breeds Microbiome (IF 15.5) Pub Date : 2024-02-20 Jiajie Sun, Fang Xie, Jing Wang, Junyi Luo, Ting Chen, Qingyan Jiang, Qianyun Xi, George E. Liu, Yongliang Zhang
Domesticated pigs serve as an ideal animal model for biomedical research and also provide the majority of meat for human consumption in China. Porcine intramuscular fat content associates with human health and diseases and is essential in pork quality. The molecular mechanisms controlling lipid metabolism and intramuscular fat accretion across tissues in pigs, and how these changes in response to pig
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Particle-attached bacteria act as gatekeepers in the decomposition of complex phytoplankton polysaccharides Microbiome (IF 15.5) Pub Date : 2024-02-20 Feng-Qing Wang, Daniel Bartosik, Chandni Sidhu, Robin Siebers, De-Chen Lu, Anke Trautwein-Schult, Dörte Becher, Bruno Huettel, Johannes Rick, Inga V. Kirstein, Karen H. Wiltshire, Thomas Schweder, Bernhard M. Fuchs, Mia M. Bengtsson, Hanno Teeling, Rudolf I. Amann
Marine microalgae (phytoplankton) mediate almost half of the worldwide photosynthetic carbon dioxide fixation and therefore play a pivotal role in global carbon cycling, most prominently during massive phytoplankton blooms. Phytoplankton biomass consists of considerable proportions of polysaccharides, substantial parts of which are rapidly remineralized by heterotrophic bacteria. We analyzed the diversity
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Correction: A tripartite bacterial-fungal-plant symbiosis in the mycorrhiza-shaped microbiome drives plant growth and mycorrhization Microbiome (IF 15.5) Pub Date : 2024-02-19 Changfeng Zhang, Marcel G. A. van der Heijden, Bethany K. Dodds, Thi Bich Nguyen, Jelle Spooren, Alain Valzano‑Held, Marco Cosme, Roeland L. Berendsen
Correction: Microbiome 12, 13 (2024) https://doi.org/10.1186/s40168-023-01726-4 Following publication of the original article [1], it was found that there were typographical errors in Figures 5-8. The term “AMFungal” should be “AM Fungal” and “colornization” should be “colonization” in those figures. The original article has been updated Zhang C, van der Heijden MGA, Dodds BK, et al. A tripartite
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Effect of a multi-strain probiotic mixture consumption on anxiety and depression symptoms induced in adult mice by postnatal maternal separation Microbiome (IF 15.5) Pub Date : 2024-02-19 Francesca De Santa, Georgios Strimpakos, Nicole Marchetti, Giorgio Gargari, Alessio Torcinaro, Stefania Arioli, Diego Mora, Carla Petrella, Stefano Farioli-Vecchioli
Intestinal microbial composition not only affects the health of the gut but also influences centrally mediated systems involved in mood, through the “gut-brain” axis, a bidirectional communication between gut microbiota and the brain. In this context, the modulation of intestinal microbiota and its metabolites through the administration of probiotics seems to represent a very promising approach in
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Gut microbiota contributes to bisphenol A-induced maternal intestinal and placental apoptosis, oxidative stress, and fetal growth restriction in pregnant ewe model by regulating gut-placental axis Microbiome (IF 15.5) Pub Date : 2024-02-17 Hao Zhang, Xia Zha, Bei Zhang, Yi Zheng, Mabrouk Elsabagh, Hongrong Wang, Mengzhi Wang
Bisphenol A (BPA) is an environmental contaminant with endocrine-disrupting properties that induce fetal growth restriction (FGR). Previous studies on pregnant ewes revealed that BPA exposure causes placental apoptosis and oxidative stress (OS) and decreases placental efficiency, consequently leading to FGR. Nonetheless, the response of gut microbiota to BPA exposure and its role in aggravating BPA-mediated
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Novel insights into the rhizosphere and seawater microbiome of Zostera marina in diverse mariculture zones Microbiome (IF 15.5) Pub Date : 2024-02-14 Hao Sun, Tianyu Wang, Shuai Liu, Xiaoyu Tang, Jie Sun, Xuerui Liu, Ye Zhao, Pingping Shen, Yanying Zhang
Seagrasses offer various ecosystem services and possess high levels of primary productivity. However, the development of mariculture has affected the homeostasis of seagrass meadow ecosystems. Plant-microbiome associations are essential for seagrasses health, but little is known about the role of environmental microbiomes and how they affect seagrass in a mariculture environment. In this study, we
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Horizontal gene transfer after faecal microbiota transplantation in adolescents with obesity Microbiome (IF 15.5) Pub Date : 2024-02-12 Anna H. Behling, Brooke C. Wilson, Daniel Ho, Wayne S. Cutfield, Tommi Vatanen, Justin M. O’Sullivan
Horizontal gene transfer (HGT) describes the transmission of DNA outside of direct ancestral lineages. The process is best characterised within the bacterial kingdom and can enable the acquisition of genetic traits that support bacterial adaptation to novel niches. The adaptation of bacteria to novel niches has particular relevance for faecal microbiota transplantation (FMT), a therapeutic procedure
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Metagenome-assembled genome reveals species and functional composition of Jianghan chicken gut microbiota and isolation of Pediococcus acidilactic with probiotic properties Microbiome (IF 15.5) Pub Date : 2024-02-12 Hongye Shen, Tinghui Wang, Weiwei Dong, Guoping Sun, Jun Liu, Nan Peng, Shumiao Zhao
Chickens are one of the most widely farmed animals worldwide and play a crucial role in meat and egg production. Gut microbiota is essential for chickens’ health, disease, growth, and egg production. However, native chickens such as Jianghan chickens have better meat and egg production quality than centralized chickens, their intestinal microbial diversity is richer, and the potential gut microbial
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Gut microbiome-metabolome interactions predict host condition Microbiome (IF 15.5) Pub Date : 2024-02-10 Oshrit Shtossel, Omry Koren, Iris Shai, Ehud Rinott, Yoram Louzoun
The effect of microbes on their human host is often mediated through changes in metabolite concentrations. As such, multiple tools have been proposed to predict metabolite concentrations from microbial taxa frequencies. Such tools typically fail to capture the dependence of the microbiome-metabolite relation on the environment. We propose to treat the microbiome-metabolome relation as the equilibrium
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Correction: Ocular mucosal homeostasis of teleost fish provides insight into the coevolution between microbiome and mucosal immunity Microbiome (IF 15.5) Pub Date : 2024-02-08 Weiguang Kong, Gaofeng Cheng, Jiafeng Cao, Jiaqian Yu, Xinyou Wang, Zhen Xu
Correction: Microbiome 12, 10 (2024) https://doi.org/10.1186/s40168-023-01716-6 Following publication of the original article [1], the author reported that Figures 3,4,5 and 9 have a yellow background and should be removed. Moreover, in the videobyte, the word „oral “ should be „ocular “ in the very first sentence of the videobyte. The original article has been updated. Kong W, Cheng G, Cao J, et al
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Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition Microbiome (IF 15.5) Pub Date : 2024-02-07 Emily M. Mercer, Hena R. Ramay, Shirin Moossavi, Isabelle Laforest-Lapointe, Myrtha E. Reyna, Allan B. Becker, Elinor Simons, Piush J. Mandhane, Stuart E. Turvey, Theo J. Moraes, Malcolm R. Sears, Padmaja Subbarao, Meghan B. Azad, Marie-Claire Arrieta
The gut microbiome undergoes primary ecological succession over the course of early life before achieving ecosystem stability around 3 years of age. These maturational patterns have been well-characterized for bacteria, but limited descriptions exist for other microbiota members, such as fungi. Further, our current understanding of the prevalence of different patterns of bacterial and fungal microbiome
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Correction: Integrating compositional and functional content to describe vaginal microbiomes in health and disease Microbiome (IF 15.5) Pub Date : 2024-02-06 Johanna B. Holm, Michael T. France, Pawel Gajer, Bing Ma, Rebecca M. Brotman, Michelle Shardell, Larry Forney, Jacques Ravel
Correction: Microbiome 11, 259 (2023) https://doi.org/10.1186/s40168-023-01692-x Following publication of the original article [1], the author reported a descripancy between the HTML and PDF version of Fig. 1. In the PDF version there were white spaces. The original article has been updated to correct this. Holm JB, France MT, Gajer P, et al. Integrating compositional and functional content to describe
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Gut microbiota-derived LCA mediates the protective effect of PEDV infection in piglets Microbiome (IF 15.5) Pub Date : 2024-02-05 Jun-Hong Xing, Tian-Ming Niu, Bo-Shi Zou, Gui-Lian Yang, Chun-Wei Shi, Qing-Song Yan, Ming-Jie Sun, Tong Yu, Shu-Min Zhang, Xi-Ze Feng, Shu-Hui Fan, Hai-Bin Huang, Jun-Hong Wang, Ming-Han Li, Yan-Long Jiang, Jian-Zhong Wang, Xin Cao, Nan Wang, Yan Zeng, Jing-Tao Hu, Di Zhang, Wu-Sheng Sun, Wen-Tao Yang, Chun-Feng Wang
The gut microbiota is a critical factor in the regulation of host health, but the relationship between the differential resistance of hosts to pathogens and the interaction of gut microbes is not yet clear. Herein, we investigated the potential correlation between the gut microbiota of piglets and their disease resistance using single-cell transcriptomics, 16S amplicon sequencing, metagenomics, and
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Early life exposure of infants to benzylpenicillin and gentamicin is associated with a persistent amplification of the gut resistome Microbiome (IF 15.5) Pub Date : 2024-02-03 Dhrati V. Patangia, Ghjuvan Grimaud, Carol-Anne O’Shea, C. A. Ryan, Eugene Dempsey, Catherine Stanton, R. Paul Ross
Infant gut microbiota is highly malleable, but the long-term longitudinal impact of antibiotic exposure in early life, together with the mode of delivery on infant gut microbiota and resistome, is not extensively studied. Two hundred and eight samples from 45 infants collected from birth until 2 years of age over five time points (week 1, 4, 8, 24, year 2) were analysed. Based on shotgun metagenomics
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Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe Microbiome (IF 15.5) Pub Date : 2024-02-03 Angela Sofia Burkhart Colorado, Alessandro Lazzaro, Charles Preston Neff, Nichole Nusbacher, Kathryn Boyd, Suzanne Fiorillo, Casey Martin, Janet C. Siebert, Thomas B. Campbell, Margaret Borok, Brent E. Palmer, Catherine Lozupone
The widespread availability of antiretroviral therapy (ART) has dramatically reduced mortality and improved life expectancy for people living with HIV (PLWH). However, even with HIV-1 suppression, chronic immune activation and elevated inflammation persist and have been linked to a pro-inflammatory gut microbiome composition and compromised intestinal barrier integrity. PLWH in urban versus rural areas
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Model-free prediction of microbiome compositions Microbiome (IF 15.5) Pub Date : 2024-02-01 Eitan E. Asher, Amir Bashan
The recent recognition of the importance of the microbiome to the host’s health and well-being has yielded efforts to develop therapies that aim to shift the microbiome from a disease-associated state to a healthier one. Direct manipulation techniques of the species’ assemblage are currently available, e.g., using probiotics or narrow-spectrum antibiotics to introduce or eliminate specific taxa. However
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Functional similarity, despite taxonomical divergence in the millipede gut microbiota, points to a common trophic strategy Microbiome (IF 15.5) Pub Date : 2024-01-29 Julius Eyiuche Nweze, Vladimír Šustr, Andreas Brune, Roey Angel
Many arthropods rely on their gut microbiome to digest plant material, which is often low in nitrogen but high in complex polysaccharides. Detritivores, such as millipedes, live on a particularly poor diet, but the identity and nutritional contribution of their microbiome are largely unknown. In this study, the hindgut microbiota of the tropical millipede Epibolus pulchripes (large, methane emitting)
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Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism Microbiome (IF 15.5) Pub Date : 2024-01-26 Luis E. Valentin-Alvarado, Sirine C. Fakra, Alexander J. Probst, Jonathan R. Giska, Alexander L. Jaffe, Luke M. Oltrogge, Jacob West-Roberts, Joel Rowland, Michael Manga, David F. Savage, Chris Greening, Brett J. Baker, Jillian F. Banfield
Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse CPR bacteria and grow in sulfide-rich springs to investigate microbial controls on biogeochemical cycling. Sulfide springs biofilms were investigated using bulk geochemical analysis, genome-resolved metagenomics
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Metagenomics reveals the temporal dynamics of the rumen resistome and microbiome in goat kids Microbiome (IF 15.5) Pub Date : 2024-01-22 Jianmin Chai, Yimin Zhuang, Kai Cui, Yanliang Bi, Naifeng Zhang
The gut microbiome of domestic animals carries antibiotic resistance genes (ARGs) which can be transmitted to the environment and humans, resulting in challenges of antibiotic resistance. Although it has been reported that the rumen microbiome of ruminants may be a reservoir of ARGs, the factors affecting the temporal dynamics of the rumen resistome are still unclear. Here, we collected rumen content
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A tripartite bacterial-fungal-plant symbiosis in the mycorrhiza-shaped microbiome drives plant growth and mycorrhization Microbiome (IF 15.5) Pub Date : 2024-01-19 Changfeng Zhang, Marcel G. A. van der Heijden, Bethany K. Dodds, Thi Bich Nguyen, Jelle Spooren, Alain Valzano-Held, Marco Cosme, Roeland L. Berendsen
Plant microbiomes play crucial roles in nutrient cycling and plant growth, and are shaped by a complex interplay between plants, microbes, and the environment. The role of bacteria as mediators of the 400-million-year-old partnership between the majority of land plants and, arbuscular mycorrhizal (AM) fungi is still poorly understood. Here, we test whether AM hyphae-associated bacteria influence the
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The fusion of multi-omics profile and multimodal EEG data contributes to the personalized diagnostic strategy for neurocognitive disorders Microbiome (IF 15.5) Pub Date : 2024-01-19 Yan Han, Xinglin Zeng, Lin Hua, Xingping Quan, Ying Chen, Manfei Zhou, Yaochen Chuang, Yang Li, Shengpeng Wang, Xu Shen, Lai Wei, Zhen Yuan, Yonghua Zhao
The increasing prevalence of neurocognitive disorders (NCDs) in the aging population worldwide has become a significant concern due to subjectivity of evaluations and the lack of precise diagnostic methods and specific indicators. Developing personalized diagnostic strategies for NCDs has therefore become a priority. Multimodal electroencephalography (EEG) data of a matched cohort of normal aging (NA)
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Host genotype, soil composition, and geo-climatic factors shape the fonio seed microbiome Microbiome (IF 15.5) Pub Date : 2024-01-17 Naheed Tabassum, Hanin Ibrahim Ahmed, Sabiha Parween, Arsheed H. Sheikh, Maged M. Saad, Simon G. Krattinger, Heribert Hirt
Fonio (Digitaria exilis), an orphan millet crop, is the oldest indigenous crop in West Africa. Although the yield is low due to pre-domestication characteristics, the quick maturation time, drought tolerance, and the ability to thrive on poor soils make fonio a climate-smart crop. Being holobionts, plants evolve in close interaction with microbial partners, which is crucial for plant phenology and
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Ocular mucosal homeostasis of teleost fish provides insight into the coevolution between microbiome and mucosal immunity Microbiome (IF 15.5) Pub Date : 2024-01-13 Weiguang Kong, Gaofeng Cheng, Jiafeng Cao, Jiaqian Yu, Xinyou Wang, Zhen Xu
The visual organ plays a crucial role in sensing environmental information. However, its mucosal surfaces are constantly exposed to selective pressures from aquatic or airborne pathogens and microbial communities. Although few studies have characterized the conjunctival-associated lymphoid tissue (CALT) in the ocular mucosa (OM) of birds and mammals, little is known regarding the evolutionary origins
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Biogeographic survey of soil bacterial communities across Antarctica Microbiome (IF 15.5) Pub Date : 2024-01-12 Gilda Varliero, Pedro H. Lebre, Byron Adams, Steven L. Chown, Peter Convey, Paul G. Dennis, Dandan Fan, Belinda Ferrari, Beat Frey, Ian D. Hogg, David W. Hopkins, Weidong Kong, Thulani Makhalanyane, Gwynneth Matcher, Kevin K. Newsham, Mark I. Stevens, Katherine V. Weigh, Don A. Cowan
Antarctica and its unique biodiversity are increasingly at risk from the effects of global climate change and other human influences. A significant recent element underpinning strategies for Antarctic conservation has been the development of a system of Antarctic Conservation Biogeographic Regions (ACBRs). The datasets supporting this classification are, however, dominated by eukaryotic taxa, with
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Determination of antibiotic resistance patterns and genotypes of Escherichia coli isolated from wild birds Microbiome (IF 15.5) Pub Date : 2024-01-08 Nejash A. Ahmed, Timur Gulhan
Curbing the potential negative impact of antibiotic resistance, one of our era's growing global public health crises, requires regular monitoring of the resistance situations, including the reservoir of resistance genes. Wild birds, a possible bioindicator of antibiotic resistance, have been suggested to play a role in the dissemination of antibiotic-resistant bacteria. Therefore, this study was conducted
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Metagenomic characterization of a novel non-ammonia-oxidizing Thaumarchaeota from hadal sediment Microbiome (IF 15.5) Pub Date : 2024-01-08 Ru-Yi Zhang, Yan-Ren Wang, Ru-Long Liu, Sung-Keun Rhee, Guo-Ping Zhao, Zhe-Xue Quan
The hadal sediment, found at an ocean depth of more than 6000 m, is geographically isolated and under extremely high hydrostatic pressure, resulting in a unique ecosystem. Thaumarchaeota are ubiquitous marine microorganisms predominantly present in hadal environments. While there have been several studies on Thaumarchaeota there, most of them have primarily focused on ammonia-oxidizing archaea (AOA)
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In-depth metaproteomics analysis of tongue coating for gastric cancer: a multicenter diagnostic research study Microbiome (IF 15.5) Pub Date : 2024-01-08 Jiahui Chen, Yingying Sun, Jie Li, Mengge Lyu, Li Yuan, Jiancheng Sun, Shangqi Chen, Can Hu, Qing Wei, Zhiyuan Xu, Tiannan Guo, Xiangdong Cheng
Our previous study revealed marked differences in tongue images between individuals with gastric cancer and those without gastric cancer. However, the biological mechanism of tongue images as a disease indicator remains unclear. Tongue coating, a major factor in tongue appearance, is the visible layer on the tongue dorsum that provides a vital environment for oral microorganisms. While oral microorganisms
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Individualized microbiotas dictate the impact of dietary fiber on colitis sensitivity Microbiome (IF 15.5) Pub Date : 2024-01-05 Erica Bonazzi, Alexis Bretin, Lucile Vigué, Fuhua Hao, Andrew D. Patterson, Andrew T. Gewirtz, Benoit Chassaing
The observation that the intestinal microbiota is central in the development of IBD suggests that dietary fiber, the microbiota’s primary source of nourishment, could play a central role in these diseases. Accordingly, enriching diets with specific soluble fibers remodels microbiota and modulates colitis sensitivity. In humans, a recent study suggests that the microbiota of select IBD patients might
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Methanolobus use unspecific methyltransferases to produce methane from dimethylsulphide in Baltic Sea sediments Microbiome (IF 15.5) Pub Date : 2024-01-03 S. L. Tsola, Y. Zhu, Y. Chen, I. A. Sanders, C. K. Economou, V. Brüchert, Ö. Eyice
In anoxic coastal and marine sediments, degradation of methylated compounds is the major route to the production of methane, a powerful greenhouse gas. Dimethylsulphide (DMS) is the most abundant biogenic organic sulphur compound in the environment and an abundant methylated compound leading to methane production in anoxic sediments. However, understanding of the microbial diversity driving DMS-dependent
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Desulfovibrio vulgaris interacts with novel gut epithelial immune receptor LRRC19 and exacerbates colitis Microbiome (IF 15.5) Pub Date : 2024-01-03 Runxiang Xie, Yu Gu, Mengfan Li, Lingfeng Li, Yunwei Yang, Yue Sun, Bingqian Zhou, Tianyu Liu, Sinan Wang, Wentian Liu, Rongcun Yang, Xiaomin Su, Weilong Zhong, Bangmao Wang, Hailong Cao
The overgrowth of Desulfovibrio, an inflammation promoting flagellated bacteria, has been found in ulcerative colitis (UC) patients. However, the molecular mechanism in promoting colitis remains unestablished. The relative abundance Desulfovibrio vulgaris (D. vulgaris) in stool samples of UC patients was detected. Mice were treated with dextran sulfate sodium to induce colitis with or without administration
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Deciphering the gut microbiome of grass carp through multi-omics approach Microbiome (IF 15.5) Pub Date : 2024-01-03 Ming Li, Hui Liang, Hongwei Yang, Qianwen Ding, Rui Xia, Jie Chen, Wenhao Zhou, Yalin Yang, Zhen Zhang, Yuanyuan Yao, Chao Ran, Zhigang Zhou
Aquaculture plays an important role in global protein supplies and food security. The ban on antibiotics as feed additive proposes urgent need to develop alternatives. Gut microbiota plays important roles in the metabolism and immunity of fish and has the potential to give rise to novel solutions for challenges confronted by fish culture. However, our understanding of fish gut microbiome is still lacking
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Unraveling the interplay between root exudates, microbiota, and rhizosheath formation in pearl millet Microbiome (IF 15.5) Pub Date : 2024-01-03 Abdelrahman Alahmad, Mourad Harir, Sylvain Fochesato, Joris Tulumello, Alesia Walker, Mohamed Barakat, Papa Mamadou Sitor Ndour, Philippe Schmitt-Kopplin, Laurent Cournac, Laurent Laplaze, Thierry Heulin, Wafa Achouak
The rhizosheath, a cohesive soil layer firmly adhering to plant roots, plays a vital role in facilitating water and mineral uptake. In pearl millet, rhizosheath formation is genetically controlled and influenced by root exudates. Here, we investigated the impact of root exudates on the microbiota composition, interactions, and assembly processes, and rhizosheath structure in pearl millet using four
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A consortia of clinical E. coli strains with distinct in vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice Microbiome (IF 15.5) Pub Date : 2023-12-20 Rachel M. Bleich, Chuang Li, Shan Sun, Ju-Hyun Ahn, Belgin Dogan, Cassandra J. Barlogio, Christopher A. Broberg, Adrienne R. Franks, Emily Bulik-Sullivan, Ian M. Carroll, Kenneth W. Simpson, Anthony A. Fodor, Janelle C. Arthur
Inflammatory bowel disease (IBD) patients experience recurrent episodes of intestinal inflammation and often follow an unpredictable disease course. Mucosal colonization with adherent-invasive Escherichia coli (AIEC) are believed to perpetuate intestinal inflammation. However, it remains unclear if the 24-year-old AIEC in vitro definition fully predicts mucosal colonization in vivo. To fill this gap
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Phylogenetic diversity of functional genes in deep-sea cold seeps: a novel perspective on metagenomics Microbiome (IF 15.5) Pub Date : 2023-12-15 Danrui Wang, Jiangtao Li, Lei Su, Wenli Shen, Kai Feng, Xi Peng, Zhujun Wang, Bo Zhao, Zheng Zhang, Zhaojing Zhang, Étienne Yergeau, Ye Deng
Leakages of cold, methane-rich fluids from subsurface reservoirs to the sea floor are termed cold seeps. Recent exploration of the deep sea has shed new light on the microbial communities in cold seeps. However, conventional metagenomic methods largely rely on reference databases and neglect the phylogeny of functional genes. In this study, we developed the REMIRGE program to retrieve the full-length
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Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients Microbiome (IF 15.5) Pub Date : 2023-12-14 Zixuan Xie, Aleix Canalda-Baltrons, Christophe d’Enfert, Chaysavanh Manichanh
The accuracy of internal-transcribed-spacer (ITS) and shotgun metagenomics has not been robustly evaluated, and the effect of diet on the composition and function of the bacterial and fungal gut microbiome in a longitudinal setting has been poorly investigated. Here we compared two approaches to study the fungal community (ITS and shotgun metagenomics), proposed an enrichment protocol to perform a