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  1. The effects of Arula-7 powder (ASP) on diarrhea and intestinal barrier function associated with its regulation of intestinal microflora in calves infected with pathogenic Escherichia coli O1 (E. coli O1) were stu...

    Authors: Hao Chen, Zhifeng Jia, Meiling He, Aorigele Chen, Xin Zhang, Jin Xu and Chunjie Wang
    Citation: Microbiome 2023 11:172
    Content type: Research Published on:

  2. Treating oral squamous cell carcinoma (OSCC) introduces new ecological environments in the oral cavity. This is expected to cause changes in the oral microbiome. The purpose of this study was to gain new infor...

    Authors: Anna I. Mäkinen, Vincent Y. Pappalardo, Mark J. Buijs, Bernd W. Brandt, Antti A. Mäkitie, Jukka H. Meurman and Egija Zaura
    Citation: Microbiome 2023 11:171
    Content type: Research Published on:

  4. Upper small intestinal dietary lipids activate a gut-brain axis regulating energy homeostasis. The prebiotic, oligofructose (OFS) improves body weight and adiposity during metabolic dysregulation but the exact...

    Authors: Savanna N. Weninger, Chloe Herman, Rachel K. Meyer, Eve T. Beauchemin, Archana Kangath, Adelina I. Lane, Taylor M. Martinez, Tahia Hasneen, Sierra A. Jaramillo, Jason Lindsey, Gayatri Vedantam, Haijiang Cai, Emily K. Cope, J. Gregory Caporaso and Frank A. Duca
    Citation: Microbiome 2023 11:169
    Content type: Research Published on:

  5. Typically, animal models studying gastrointestinal microbiotas compromised in early life have employed either germ-free animals or mice treated with a cocktail of antibiotics. Such studies intend to mimic scen...

    Authors: Emily C. Hoedt, Cara M. Hueston, Nora Cash, Roger S. Bongers, Jonathan M. Keane, Kees van Limpt, Kaouther Ben Amor, Jan Knol, John MacSharry and Douwe van Sinderen
    Citation: Microbiome 2023 11:168
    Content type: Research Published on:

  6. Legionella are parasites of freshwater protozoa, responsible for Legionellosis. Legionella can be found in a variety of aquatic environments, including rivers, lakes, and springs, as well as in engineered water s...

    Authors: Oded Bergman, Yaron Be’eri-Shlevin and Shira Ninio
    Citation: Microbiome 2023 11:167
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2023 11:177

  7. The resistome, the collection of antibiotic resistance genes (ARGs) in a microbiome, is increasingly recognised as relevant to the development of clinically relevant antibiotic resistance. Many metagenomic stu...

    Authors: Simen Fredriksen, Stef de Warle, Peter van Baarlen, Jos Boekhorst and Jerry M. Wells
    Citation: Microbiome 2023 11:166
    Content type: Research Published on:

  8. During development, elevated levels of maternal glucocorticoids (GCs) can have detrimental effects on offspring morphology, cognition, and behavior as well as physiology and metabolism. Depending on the timing...

    Authors: Simone Anzà, Dominik Schneider, Rolf Daniel, Michael Heistermann, Somboon Sangmaneedet, Julia Ostner and Oliver Schülke
    Citation: Microbiome 2023 11:165
    Content type: Research Published on:

  9. Emerging evidence suggests the potential mediating role of microbiome in health disparities. However, no analytic framework can be directly used to analyze microbiome as a mediator between health disparity and...

    Authors: Chan Wang, Jiyoung Ahn, Thaddeus Tarpey, Stella S. Yi, Richard B. Hayes and Huilin Li
    Citation: Microbiome 2023 11:164
    Content type: Methodology Published on:

  10. Antibiotics are widely used for prophylactic therapy and for improving the growth performance of chicken. The problem of bacterial drug resistance caused by antibiotic abuse has previously attracted extensive ...

    Authors: Xianghui Liang, Zhipeng Zhang, Hai Wang, Xingbang Lu, Wen Li, Haoran Lu, Ayan Roy, Xuejuan Shen, David M. Irwin and Yongyi Shen
    Citation: Microbiome 2023 11:163
    Content type: Research Published on:

  11. Darier’s disease (DD) is a genodermatosis caused by mutations of the ATP2A2 gene leading to disrupted keratinocyte adhesion. Recurrent episodes of skin inflammation and infections with a typical malodour in DD in...

    Authors: Yacine Amar, Danielle Rogner, Rafaela L. Silva, Bärbel U. Foesel, Minhaz Ud-Dean, Ilias Lagkouvardos, Susanne A. Steimle-Grauer, Sebastian Niedermeier, Susanne Kublik, Manja Jargosch, Matthias Heinig, Jenny Thomas, Stefanie Eyerich, Jakob D. Wikström, Michael Schloter, Kilian Eyerich…
    Citation: Microbiome 2023 11:162
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2023 11:206

  12. Porphyromonas gingivalis (hereafter “Pg”) is an oral pathogen that has been hypothesized to act as a keystone driver of inflammation and periodontal disease. Although Pg is most readily recovered from individuals...

    Authors: Cole B. Matrishin, Elaine M. Haase, Floyd E. Dewhirst, Jessica L. Mark Welch, Fabiola Miranda-Sanchez, Tsute Chen, Donald C. MacFarland and Kathryn M. Kauffman
    Citation: Microbiome 2023 11:161
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2024 12:144

  13. Ferromanganese nodule-bearing deep-sea sediments cover vast areas of the ocean floor, representing a distinctive habitat in the abyss. These sediments harbor unique conditions characterized by high iron concen...

    Authors: Dechao Zhang, Xudong Li, Yuehong Wu, Xuewei Xu, Yanxia Liu, Benze Shi, Yujie Peng, Dadong Dai, Zhongli Sha and Jinshui Zheng
    Citation: Microbiome 2023 11:160
    Content type: Research Published on:

  14. Cervicovaginal inflammation has been linked to negative reproductive health outcomes including the acquisition of HIV, other sexually transmitted infections, and cervical carcinogenesis. While changes to the v...

    Authors: Christina Farr Zuend, Alana Lamont, Laura Noel-Romas, Samantha Knodel, Kenzie Birse, Kateryna Kratzer, Peter McQueen, Michelle Perner, Hossaena Ayele, Sarah Mutch, Alicia R. Berard, John J. Schellenberg, Faruk Senturk, Stuart McCorrister, Garrett Westmacott, Fran Mulhall…
    Citation: Microbiome 2023 11:159
    Content type: Research Published on:

  15. Bovine respiratory disease (BRD) is one of the most common diseases in intensively managed cattle, often resulting in high morbidity and mortality. Although several pathogens have been isolated and extensively...

    Authors: Barbara P. Brito, Melinda J. Frost, Kay Anantanawat, Frederick Jaya, Tony Batterham, Steven P. Djordjevic, Wei-Shan Chang, Edward C. Holmes, Aaron E. Darling and Peter D. Kirkland
    Citation: Microbiome 2023 11:158
    Content type: Research Published on:

  16. Secondary bacterial infections and pneumonia are major mortality causes of respiratory viruses, and the disruption of the upper respiratory tract (URT) microbiota is a crucial component of this process. Howeve...

    Authors: Hui Li, Xiaorong Wu, Hong Zeng, Bozhen Chang, Ying Cui, Jingxiang Zhang, Ruixia Wang and Tao Ding
    Citation: Microbiome 2023 11:157
    Content type: Research Published on:

  17. Ticks can transmit a broad variety of pathogens of medical importance, including Borrelia afzelii, the causative agent of Lyme borreliosis in Europe. Tick microbiota is an important factor modulating, not only ve...

    Authors: Alejandra Wu-Chuang, Lourdes Mateos-Hernandez, Apolline Maitre, Ryan O. M. Rego, Radek Šíma, Stefania Porcelli, Sabine Rakotobe, Angélique Foucault-Simonin, Sara Moutailler, Vaidas Palinauskas, Justė Aželytė, Ladislav Sǐmo, Dasiel Obregon and Alejandro Cabezas-Cruz
    Citation: Microbiome 2023 11:151
    Content type: Research Published on:

  19. For more than a century, the Koch’s postulates have been the golden rule for determining the causative agents in diseases. However, in cases of multiple pathogens-one disease, in which different pathogens can ...

    Authors: Dongwei Hou, Taixin Lian, Guangyu Guo, Han Gong, Chengcheng Wu, Peiyun Han, Shaoping Weng and Jianguo He
    Citation: Microbiome 2023 11:155
    Content type: Research Published on:

  20. Aberrant tryptophan (Trp)-kynurenine (Kyn) metabolism has been implicated in the pathogenesis of human disease. In particular, populations with long-term western-style diets are characterized by an excess of K...

    Authors: Penghao Sun, Mengli Wang, Yong-Xin Liu, Luqi Li, Xuejun Chai, Wei Zheng, Shulin Chen, Xiaoyan Zhu and Shanting Zhao
    Citation: Microbiome 2023 11:154
    Content type: Research Published on:

  21. Lactobacillus species in gut microbiota shows great promise in alleviation of metabolic diseases. However, little is known about the molecular mechanism of how Lactobacillus interacts with metabolites in circulat...

    Authors: Mengfan Li, Xiaoling Wu, Zewang Guo, Ruichen Gao, Zifu Ni, Hualing Cui, Minhua Zong, Filip Van Bockstaele and Wenyong Lou
    Citation: Microbiome 2023 11:153
    Content type: Research Published on:

  22. Microbes constitute almost the entire biological community in subsurface groundwater and play an important role in ecological evolution and global biogeochemical cycles. Ecological baseline as a fundamental re...

    Authors: Sining Zhong, Shungui Zhou, Shufeng Liu, Jiawen Wang, Chenyuan Dang, Qian Chen, Jinyun Hu, Shanqing Yang, Chunfang Deng, Wenpeng Li, Juan Liu, Alistair G. L. Borthwick and Jinren Ni
    Citation: Microbiome 2023 11:152
    Content type: Research Published on:

  23. Individuals that band together create new ecological opportunities for microorganisms. In vertical transmission, theory predicts a conserved microbiota within lineages, especially social bees. Bees exhibit sol...

    Authors: Jordan G. Kueneman, Ernesto Bonadies, Devin Thomas, David W. Roubik and William T. Wcislo
    Citation: Microbiome 2023 11:150
    Content type: Research Published on:

  24. The human gut microbiota is a complex community comprised of trillions of bacteria and is critical for the digestion and absorption of nutrients. Bacterial communities of the intestinal microbiota influence th...

    Authors: Aravindh Nagarajan, Kristin Scoggin, Jyotsana Gupta, David W. Threadgill and Helene L. Andrews-Polymenis
    Citation: Microbiome 2023 11:149
    Content type: Research Published on:

  25. Gut microbiota have a complex role on the survivability, digestive physiology, production, and growth performance in animals. Recent studies have emphasized the effects of prebiotics therapy on the gut disease...

    Authors: Tingbei Bo, He Liu, Min Liu, Qiyong Liu, Qingduo Li, Yipeng Cong, Yi Luo, Yuqi Wang, Bo Yu, Tianchun Pu, Lu Wang, Zheng Wang and Dehua Wang
    Citation: Microbiome 2023 11:148
    Content type: Brief Report Published on:

  26. Following solid organ transplantation, tacrolimus (TAC) is an essential drug in the immunosuppressive strategy. Its use constitutes a challenge due to its narrow therapeutic index and its high inter- and intra...

    Authors: Alexandra L. Degraeve, Vincent Haufroid, Axelle Loriot, Laurent Gatto, Vanessa Andries, Lars Vereecke, Laure Elens and Laure B. Bindels
    Citation: Microbiome 2023 11:138
    Content type: Research Published on:

  27. Understanding how the host’s microbiome shapes phenotypes and participates in the host response to selection is fundamental for evolutionists and animal and plant breeders. Currently, selection for resilience ...

    Authors: Cristina Casto-Rebollo, María José Argente, María Luz García, Ramona Natacha Pena, Agustín Blasco and Noelia Ibáñez-Escriche
    Citation: Microbiome 2023 11:147
    Content type: Research Published on:

  28. Despite the knowledge that the soil–plant–microbiome nexus is shaped by interactions amongst its members, very little is known about how individual symbioses regulate this shaping. Even less is known about how...

    Authors: Beatriz Lagunas, Luke Richards, Chrysi Sergaki, Jamie Burgess, Alonso Javier Pardal, Rana M. F. Hussain, Bethany L. Richmond, Laura Baxter, Proyash Roy, Anastasia Pakidi, Gina Stovold, Saúl Vázquez, Sascha Ott, Patrick Schäfer and Miriam L. Gifford
    Citation: Microbiome 2023 11:146
    Content type: Research Published on:

  29. Most interactions between the host and its microbiota occur at the gut barrier, and primary colonizers are essential in the gut barrier maturation in the early life. The mother–offspring transmission of microo...

    Authors: M. Barone, Y. Ramayo-Caldas, J. Estellé, K. Tambosco, S. Chadi, F. Maillard, M. Gallopin, J. Planchais, F. Chain, C. Kropp, D. Rios-Covian, H. Sokol, P. Brigidi, P. Langella and R. Martín
    Citation: Microbiome 2023 11:140
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2023 11:173

  30. Adolescent depression is becoming one of the major public health concerns, because of its increased prevalence and risk of significant functional impairment and suicidality. Clinical depression commonly emerge...

    Authors: Manfei Zhou, Yichun Fan, Liuting Xu, Zheng Yu, Sizhe Wang, Huaisha Xu, Jiuping Zhang, Linwei Zhang, Wenwei Liu, Linlin Wu, Jing Yu, Honghong Yao, Jun Wang and Rong Gao
    Citation: Microbiome 2023 11:145
    Content type: Research Published on:

  31. Marine prokaryotes are a rich source of novel bioactive secondary metabolites for drug discovery. Recent genome mining studies have revealed their great potential to bio-synthesize novel secondary metabolites....

    Authors: Bin Wei, Gang-Ao Hu, Zhen-Yi Zhou, Wen-Chao Yu, Ao-Qi Du, Cai-Ling Yang, Yan-Lei Yu, Jian-Wei Chen, Hua-Wei Zhang, Qihao Wu, Qi Xuan, Xue-Wei Xu and Hong Wang
    Citation: Microbiome 2023 11:144
    Content type: Research Published on:

  32. Whole microbiome RNASeq (metatranscriptomics) has emerged as a powerful technology to functionally interrogate microbial communities. A key challenge is how best to process, analyze, and interpret these comple...

    Authors: Billy Taj, Mobolaji Adeolu, Xuejian Xiong, Jordan Ang, Nirvana Nursimulu and John Parkinson
    Citation: Microbiome 2023 11:143
    Content type: Software Published on:

  33. Phosphonates are the main components in the global phosphorus redox cycle. Little is known about phosphonate metabolism in freshwater ecosystems, although rapid consumption of phosphonates has been observed fr...

    Authors: Liang Zhao, Li-Zhou Lin, Ying Zeng, Wen-Kai Teng, Meng-Yun Chen, Jerry J. Brand, Ling-Ling Zheng, Nan-Qin Gan, Yong-Hui Gong, Xin-Yi Li, Jin Lv, Ting Chen, Bo-Ping Han, Li-Rong Song and Wen-Sheng Shu
    Citation: Microbiome 2023 11:142
    Content type: Research Published on:

  34. Infants receive their first bacteria from their birthing parent. This newly acquired microbiome plays a pivotal role in developing a robust immune system, the cornerstone of long-term health.

    Authors: Heidi K. Leftwich, Daniela Vargas-Robles, Mayra Rojas-Correa, Yan Rou Yap, Shakti Bhattarai, Doyle V. Ward, Gavin Fujimori, Catherine S. Forconi, Tracy Yeboah, Acara Carter, Alyssa Kastrinakis, Alison M. Asirwatham, Vanni Bucci, Ann M. Moormann and Ana Maldonado-Contreras
    Citation: Microbiome 2023 11:141
    Content type: Research Published on:

  35. Keystone taxa are drivers of microbiome structure and functioning, which may play critical roles in microbiome-level responses to recalcitrant pollution and are a key to bioremediation. However, the characteri...

    Authors: Xiaolan Lin, Baoyi Qiao, Ruirui Chang, Yixin Li, Wei Zheng, Zhili He and Yun Tian
    Citation: Microbiome 2023 11:139
    Content type: Research Published on:

  36. Intestinal inflammation has become a threatening concern in chicken production worldwide and is closely associated with Th17/Treg cell imbalance. Several studies described that gut microbiota is significantly ...

    Authors: Ziyu Ma, Muhammad Akhtar, Hong Pan, Qiyao Liu, Yan Chen, Xinxin Zhou, Yingting You, Deshi Shi and Huazhen Liu
    Citation: Microbiome 2023 11:137
    Content type: Research Published on:

  37. Disruption of the microbial community in the respiratory tract due to infections, like influenza, could impact transmission of bacterial pathogens. Using samples from a household study, we determined whether m...

    Authors: Lingdi Zhang, Jahan Rahman, Matthew Chung, Lauren Lashua, Aubree Gordon, Angel Balmaseda, Guillermina Kuan, Richard Bonneau and Elodie Ghedin
    Citation: Microbiome 2023 11:136
    Content type: Research Published on:

  38. Pathogen infections seriously affect host health, and the use of antibiotics increases the risk of the emergence of drug-resistant bacteria and also increases environmental and health safety risks. Probiotics ...

    Authors: Xiaozhou Qi, Yong Zhang, Yilin Zhang, Fei Luo, Kaige Song, Gaoxue Wang and Fei Ling
    Citation: Microbiome 2023 11:135
    Content type: Research Published on:

  39. Marine heterotrophic flagellates (HF) are dominant bacterivores in the ocean, where they represent the trophic link between bacteria and higher trophic levels and participate in the recycling of inorganic nutr...

    Authors: Aleix Obiol, David López-Escardó, Eric D. Salomaki, Monika M. Wiśniewska, Irene Forn, Elisabet Sà, Dolors Vaqué, Martin Kolísko and Ramon Massana
    Citation: Microbiome 2023 11:134
    Content type: Research Published on:

  40. Hydrogen gas (H2) is a common product of carbohydrate fermentation in the human gut microbiome and its accumulation can modulate fermentation. Concentrations of colonic H2 vary between individuals, raising the po...

    Authors: Austin Campbell, Kristi Gdanetz, Alexander W. Schmidt and Thomas M. Schmidt
    Citation: Microbiome 2023 11:133
    Content type: Research Published on:

  41. Cystic Fibrosis (CF) is a genetic condition characterized by neutrophilic inflammation and recurrent infection of the airways. How these processes are initiated and perpetuated in CF remains largely unknown. W...

    Authors: Jose A. Caparrós-Martín, Montserrat Saladie, S. Patricia Agudelo-Romero, F. Jerry Reen, Robert S. Ware, Peter D. Sly, Stephen M. Stick and Fergal O’Gara
    Citation: Microbiome 2023 11:132
    Content type: Research Published on:

  42. Characterization of microbial activity is essential to the understanding of the basic biology of microbial communities, as the function of a microbiome is defined by its biochemically active (“viable”) communi...

    Authors: Ya Wang, Kelsey N. Thompson, Yan Yan, Meghan I. Short, Yancong Zhang, Eric A. Franzosa, Jiaxian Shen, Erica M. Hartmann and Curtis Huttenhower
    Citation: Microbiome 2023 11:131
    Content type: Research Published on:

  43. Nudibranchs comprise a group of > 6000 marine soft-bodied mollusk species known to use secondary metabolites (natural products) for chemical defense. The full diversity of these metabolites and whether symbiot...

    Authors: Mária Džunková, James J. La Clair, Tomáš Tyml, Devin Doud, Frederik Schulz, Samuel Piquer-Esteban, Dafne Porcel Sanchis, Andrew Osborn, David Robinson, Katherine B. Louie, Ben P. Bowen, Robert M. Bowers, Janey Lee, Vicente Arnau, Wladimiro Díaz-Villanueva, Ramunas Stepanauskas…
    Citation: Microbiome 2023 11:130
    Content type: Research Published on:

  44. Humans emit approximately 30 million microbial cells per hour into their immediate vicinity. However, sampling of aerosolized microbial taxa (aerobiome) remains largely uncharacterized due to the complexity an...

    Authors: Jarrad T. Hampton-Marcell, Aritra Ghosh, Mohamad Jafari Gukeh and Constantine M. Megaridis
    Citation: Microbiome 2023 11:129
    Content type: Research Published on:

  45. Listeria monocytogenes can survive in cold and wet environments, such as tree fruit packing facilities and it has been implicated in outbreaks and recalls of tree fruit products. However, little is known about mi...

    Authors: M. Laura Rolon, Xiaoqing Tan, Taejung Chung, Narjol Gonzalez-Escalona, Yi Chen, Dumitru Macarisin, Luke F. LaBorde and Jasna Kovac
    Citation: Microbiome 2023 11:128
    Content type: Research Published on:

  46. Bacteria colonizing the nasopharynx play a key role as gatekeepers of respiratory health. Yet, dynamics of early life nasopharyngeal (NP) bacterial profiles remain understudied in low- and middle-income countr...

    Authors: Shantelle Claassen-Weitz, Sugnet Gardner-Lubbe, Yao Xia, Kilaza S. Mwaikono, Stephanie Harris Mounaud, William C. Nierman, Lesley Workman, Heather J. Zar and Mark P. Nicol
    Citation: Microbiome 2023 11:127
    Content type: Research Published on:

  47. Macroalgal epiphytic microbial communities constitute a rich resource for novel enzymes and compounds, but studies so far largely focused on tag-based microbial diversity analyses or limited metagenome sequenc...

    Authors: De-Chen Lu, Feng-Qing Wang, Rudolf I. Amann, Hanno Teeling and Zong-Jun Du
    Citation: Microbiome 2023 11:126
    Content type: Research Published on:

  48. Several investigations on the microbial diversity and functional properties of the International Space Station (ISS) environment were carried out to understand the influence of spaceflight conditions on the mi...

    Authors: Nitin K. Singh, Jason M. Wood, Jose Patane, Livia Maria Silva Moura, Jonathan Lombardino, João Carlos Setubal and Kasthuri Venkateswaran
    Citation: Microbiome 2023 11:125
    Content type: Research Published on:

  49. The effects of air pollutants, particularly polycyclic aromatic hydrocarbons (PAHs), on the skin microbiome remain poorly understood. Thus, to better understand the interplay between air pollutants, microbiome...

    Authors: Marcus H. Y. Leung, Xinzhao Tong, Zhiyong Shen, Shicong Du, Philippe Bastien, Brice M. R. Appenzeller, Richard J. Betts, Sakina Mezzache, Nasrine Bourokba, Nukhet Cavusoglu, Luc Aguilar, Namita Misra, Cécile Clavaud and Patrick K. H. Lee
    Citation: Microbiome 2023 11:124
    Content type: Research Published on:

  50. Dental caries is a microbe and sugar-mediated biofilm-dependent oral disease. Of particular significance, a virulent type of dental caries, known as severe early childhood caries (S-ECC), is characterized by t...

    Authors: Yuan Liu, Scott G. Daniel, Hye-Eun Kim, Hyun Koo, Jonathan Korostoff, Flavia Teles, Kyle Bittinger and Geelsu Hwang
    Citation: Microbiome 2023 11:123
    Content type: Research Published on:
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