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Microbiome

This section welcomes studies on fundamental and clinical aspects of microbiome research including but not limited to gut and tissue microbiomes, human, animal, plant, and environmental microbiomes. It also welcomes studies on host-microbiome interactions and the impact of microbiome on disease occurrence, prognosis and treatment. This section also aims to be the home for new methodological advances in the study of microbiomes.

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  1. To understand inter-individual variability of fecal microbe transplantation (FMT) to enhance anti-PD-1 immunotherapy (IT) for melanoma, we analyzed the data sets from two recent publications with a microbial s...

    Authors: Hyunmin Koo and Casey D. Morrow

    Citation: BMC Microbiology 2021 21:251

    Content type: Research article

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  2. Infants with cystic fibrosis (CF) suffer from gastrointestinal (GI) complications, including pancreatic insufficiency and intestinal inflammation, which have been associated with impaired nutrition and growth....

    Authors: Alexander Eng, Hillary S. Hayden, Christopher E. Pope, Mitchell J. Brittnacher, Anh T. Vo, Eli J. Weiss, Kyle R. Hager, Daniel H. Leung, Sonya L. Heltshe, Daniel Raftery, Samuel I. Miller, Lucas R. Hoffman and Elhanan Borenstein

    Citation: BMC Microbiology 2021 21:247

    Content type: Research article

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  3. The infant intestinal microbiome plays an important role in metabolism and immune development with impacts on lifelong health. The linkage between the taxonomic composition of the microbiome and its metabolic ...

    Authors: Quang P. Nguyen, Margaret R. Karagas, Juliette C. Madan, Erika Dade, Thomas J. Palys, Hilary G. Morrison, Wimal W. Pathmasiri, Susan McRitche, Susan J. Sumner, H. Robert Frost and Anne G. Hoen

    Citation: BMC Microbiology 2021 21:238

    Content type: Research article

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  4. Modulating the microbiota is a leading-edge strategy for the restoration and maintenance of a healthy, balanced environment. The use of health-promoting bacteria has demonstrated some potential benefits as an ...

    Authors: Veronica Moskovicz, Rina Ben-El, Guy Horev and Boaz Mizrahi

    Citation: BMC Microbiology 2021 21:231

    Content type: Research article

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  5. Gut microbiota (GMB) alteration has been reported to influence the Alzheimer’s disease (AD) pathogenesis through immune, endocrine, and metabolic pathways. This study aims to investigate metabolic output of th...

    Authors: Jianxiong Xi, Ding Ding, Huiwei Zhu, Ruru Wang, Feng Su, Wanqing Wu, Zhenxu Xiao, Xiaoniu Liang, Qianhua Zhao, Zhen Hong, Hua Fu and Qianyi Xiao

    Citation: BMC Microbiology 2021 21:226

    Content type: Research article

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  6. Staphylococci are important members of the human skin microbiome. Many staphylococcal species and strains are commensals of the healthy skin microbiota, while few play essential roles in skin diseases such as ...

    Authors: Charlotte Marie Ahle, Kristian Stødkilde-Jørgensen, Anja Poehlein, Wolfgang R. Streit, Jennifer Hüpeden and Holger Brüggemann

    Citation: BMC Microbiology 2021 21:221

    Content type: Methodology article

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  7. The high incidence of bacterial genes that confer resistance to last-resort antibiotics, such as colistin, caused by mobilized colistin resistance (mcr) genes, poses an unprecedented threat to human health. Under...

    Authors: Bruno G. N. Andrade, Tobias Goris, Haithem Afli, Felipe H. Coutinho, Alberto M. R. Dávila and Rafael R. C. Cuadrat

    Citation: BMC Microbiology 2021 21:220

    Content type: Research article

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  8. Accumulating evidence have shown that the intestinal microbiota plays an important role in prevention of host obesity and metabolism disorders. Recent studies also demonstrate that early life is the key time f...

    Authors: Z. H. Miao, W. X. Zhou, R. Y. Cheng, H. J. Liang, F. L. Jiang, X. Shen, J. H. Lu, M. Li and F. He

    Citation: BMC Microbiology 2021 21:209

    Content type: Research article

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  9. The human gut microbiome harbors a collection of bacterial antimicrobial resistance genes (ARGs) known as the resistome. The factors associated with establishment of the resistome in early life are not well un...

    Authors: Rebecca M. Lebeaux, Modupe O. Coker, Erika F. Dade, Thomas J. Palys, Hilary G. Morrison, Benjamin D. Ross, Emily R. Baker, Margaret R. Karagas, Juliette C. Madan and Anne G. Hoen

    Citation: BMC Microbiology 2021 21:201

    Content type: Research article

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  10. The compromised gut microbiome that results from C-section birth has been hypothesized as a risk factor for the development of non-communicable diseases (NCD). In a double-blind randomized controlled study, 15...

    Authors: Christophe Lay, Collins Wenhan Chu, Rikky Wenang Purbojati, Enzo Acerbi, Daniela I. Drautz-Moses, Paola Florez de Sessions, Song Jie, Eliza Ho, Yee Jiun Kok, Xuezhi Bi, Shuwen Chen, Shi Ya Mak, Mei Chien Chua, Anne E. N. Goh, Wen Chin Chiang, Rajeshwar Rao…

    Citation: BMC Microbiology 2021 21:191

    Content type: Research article

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  11. With increasing concerns about the impact of frequent antibiotic usage on the human microbiome, it is important to characterize the potential for such effects in early antibiotic drug development clinical tria...

    Authors: Andrea Nuzzo, Stephanie Van Horn, Christopher Traini, Caroline R. Perry, Etienne F. Dumont, Nicole E. Scangarella-Oman, David F. Gardiner and James R. Brown

    Citation: BMC Microbiology 2021 21:181

    Content type: Research article

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  12. Human well-being has been linked to the composition and functional capacity of the intestinal microbiota. As regular exercise is known to improve human health, it is not surprising that exercise was previously...

    Authors: Lucas Moitinho-Silva, Michelle Wegener, Sandra May, Florian Schrinner, Awais Akhtar, Teide J. Boysen, Eva Schaeffer, Clint Hansen, Timo Schmidt, Malte C. Rühlemann, Matthias Hübenthal, Philipp Rausch, Mustafa T. Kondakci, Walter Maetzler, Stephan Weidinger, Matthias Laudes…

    Citation: BMC Microbiology 2021 21:162

    Content type: Research article

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  13. New developments in next-generation sequencing technologies and massive data received from this approach open wide prospects for personalised medicine and nutrition studies. Metagenomic analysis of the gut mic...

    Authors: Jekaterina Kazantseva, Esther Malv, Aleksei Kaleda, Aili Kallastu and Anne Meikas

    Citation: BMC Microbiology 2021 21:158

    Content type: Research article

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  14. Inter-individual variations in gut microbiota composition are observed even among healthy populations. The gut microbiota may exhibit a unique composition depending on the country of origin and race of individ...

    Authors: Jonguk Park, Kumiko Kato, Haruka Murakami, Koji Hosomi, Kumpei Tanisawa, Takashi Nakagata, Harumi Ohno, Kana Konishi, Hitoshi Kawashima, Yi-An Chen, Attayeb Mohsen, Jin-zhong Xiao, Toshitaka Odamaki, Jun Kunisawa, Kenji Mizuguchi and Motohiko Miyachi

    Citation: BMC Microbiology 2021 21:151

    Content type: Research article

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  15. Immunosuppression during liver transplantation (LT) enables the prevention and treatment of organ rejection but poses a risk for severe infectious diseases. Immune modulation and antimicrobials affect the plas...

    Authors: Toshihiko Okumura, Kazuhiro Horiba, Hideya Kamei, Suguru Takeuchi, Takako Suzuki, Yuka Torii, Jun-ichi Kawada, Yoshiyuki Takahashi, Yasuhiro Ogura, Tomoo Ogi and Yoshinori Ito

    Citation: BMC Microbiology 2021 21:104

    Content type: Research article

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  16. Composition and maintenance of the microbiome is vital to gut homeostasis. However, there is limited knowledge regarding the impact of high doses of radiation, which can occur as a result of cancer radiation t...

    Authors: Raj Kalkeri, Kevin Walters, William Van Der Pol, Braden C. McFarland, Nathan Fisher, Fusataka Koide, Casey D. Morrow and Vijay K. Singh

    Citation: BMC Microbiology 2021 21:93

    Content type: Research article

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  17. High-risk human papilloma virus (hrHPV) is the main causal factor of cervical precancer and cancer when persistent infection is left untreated. Previous studies have confirmed the vaginal microbiota is associa...

    Authors: Zhan Zhang, Ting Li, Dai Zhang, Xiaonan Zong, Huihui Bai, Hui Bi and Zhaohui Liu

    Citation: BMC Microbiology 2021 21:90

    Content type: Research article

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  18. The microbiota of the lower respiratory tract in patients with non-tuberculous mycobacterial pulmonary disease (NTM-PD) has not been fully evaluated. We explored the role of the lung microbiota in NTM-PD by an...

    Authors: Sung-Yoon Kang, Hyojung Kim, Sungwon Jung, Sang Min Lee and Sang Pyo Lee

    Citation: BMC Microbiology 2021 21:84

    Content type: Research article

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  19. A diverse community of microbes naturally exists on the phylloplane, the surface of leaves. It is one of the most prevalent microbial habitats on earth and bacteria are the most abundant members, living in com...

    Authors: Vincent Stevens, Sofie Thijs and Jaco Vangronsveld

    Citation: BMC Microbiology 2021 21:66

    Content type: Research article

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  20. To date, information on healthy female urinary microbiota is available mostly at genus level and at one time point. However, profound species-level characterization of healthy urinary microbiome and its stabil...

    Authors: Magdalena Ksiezarek, Svetlana Ugarcina-Perovic, Joana Rocha, Filipa Grosso and Luísa Peixe

    Citation: BMC Microbiology 2021 21:64

    Content type: Research article

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  21. Stool metabolites provide essential insights into the function of the gut microbiome. The current gold standard for storage of stool samples for metabolomics is flash-freezing at − 80 °C which can be inconveni...

    Authors: Sivapriya Ramamoorthy, Shira Levy, Masouma Mohamed, Alaa Abdelghani, Anne M. Evans, Luke A. D. Miller, Lopa Mehta, Sean Moore, Elizaveta Freinkman and Suchitra K. Hourigan

    Citation: BMC Microbiology 2021 21:59

    Content type: Research article

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  22. Medical film dressings have been used to obtain skin microbiota for skin microbiome studies, although their adhesive force may be so strong that the skin could be injured when applied to those who have fragile...

    Authors: Kazuhiro Ogai, Kana Shibata, Natsuki Takahashi, Kohei Ogura, Shigefumi Okamoto and Junko Sugama

    Citation: BMC Microbiology 2021 21:54

    Content type: Research article

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  23. Gut microbiota is critical in maintaining human health, of which diversity and abundance are subject to significantly reduce in seniors. Gut microbiota is reported to be stable across the long adulthood in gen...

    Authors: Junkui Chen, Xionge Pi, Wei Liu, Qunfang Ding, Xin Wang, Weiguo Jia and Liying Zhu

    Citation: BMC Microbiology 2021 21:47

    Content type: Research article

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  24. The microbiota plays an important role in host health. Although rubidium (Rb) has been used to study its effects on depression and cancers, the interaction between microbial commensals and Rb is still unexplor...

    Authors: Qian Chen, Zhiguo He, Yuting Zhuo, Shuzhen Li, Wenjing Yang, Liang Hu and Hui Zhong

    Citation: BMC Microbiology 2021 21:46

    Content type: Research article

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  25. The proliferation and survival of microbial organisms including intestinal microbes are determined by their surrounding environments. Contrary to popular myth, the nutritional and chemical compositions, water ...

    Authors: Enkhchimeg Lkhagva, Hea-Jong Chung, Jinny Hong, Wai Hong Wilson Tang, Sang-Il Lee, Seong-Tshool Hong and Seungkoo Lee

    Citation: BMC Microbiology 2021 21:44

    Content type: Research article

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  26. Studies of the gut microbiome are becoming increasingly important. Such studies require stool collections that can be processed or frozen in a timely manner so as not to alter the microbial content. Due to the...

    Authors: Meghan I. Short, Robert Hudson, Benjamin D. Besasie, Kelly R. Reveles, Dimpy P. Shah, Susannah Nicholson, Teresa L. Johnson-Pais, Korri Weldon, Zhao Lai, Robin J. Leach, Bernard Fongang and Michael A. Liss

    Citation: BMC Microbiology 2021 21:26

    Content type: Research article

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  27. The porcine respiratory tract harbours multiple microorganisms, and the interactions between these organisms could be associated with animal health status. Pasteurella multocida is a culturable facultative anaero...

    Authors: Nonzee Hanchanachai, Pramote Chumnanpuen and Teerasak E-kobon

    Citation: BMC Microbiology 2021 21:19

    Content type: Research article

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  28. The gut microbiome is essential for the host’s health and serves as an essential reservoir of antibiotic resistance genes (ARGs). We investigated the effects of different factors, including the dietary shifts ...

    Authors: Ghulam Raza Mustafa, Caiwu Li, Siyue Zhao, Lei Jin, Xueping He, Muhammad Zubair Shabbir, Yongguo He, Ti Li, Wenwen Deng, Lin Xu, Yaowu Xiong, Guiquan Zhang, Hemin Zhang, Yan Huang and Likou Zou

    Citation: BMC Microbiology 2021 21:15

    Content type: Research article

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  29. Although gut microbiota dysbiosis has been reported in HIV infected individuals recently, the relationship between the gut microbiota and immune activation in patients with different immune responses to highly...

    Authors: Yirui Xie, Jia Sun, Li Wei, Haiyin Jiang, Caiqin Hu, Jiezuan Yang, Ying Huang, Bing Ruan and Biao Zhu

    Citation: BMC Microbiology 2021 21:11

    Content type: Research article

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  30. Working in an underground tunnel environment is unavoidable in professions such as miners and tunnel workers, and there is a concern about the health of these workers. Few studies have addressed alterations in...

    Authors: Zhen-Hua Lu, Yi-Wen Liu, Zhao-Hua Ji, Ting Fu, Min Yan, Zhong-jun Shao and Yong Long

    Citation: BMC Microbiology 2021 21:7

    Content type: Research article

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  31. Although generally known as a human commensal, Staphylococcus epidermidis is also an opportunistic pathogen that can cause nosocomial infections related to foreign body materials and immunocompromized patients. I...

    Authors: Amalie Katrine Rendboe, Thor Bech Johannesen, Anna Cäcilia Ingham, Emeli Månsson, Søren Iversen, Sharmin Baig, Sofie Edslev, Jørgen Skov Jensen, Bo Söderquist, Paal Skytt Andersen and Marc Stegger

    Citation: BMC Microbiology 2020 20:362

    Content type: Methodology article

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  32. In the past decade, the initial studies of the gut microbiota started focusing on the correlation of the composition of the gut microbiota and the health or diseases of the host, and there are extensive litera...

    Authors: Nesreen H. Aljahdali, Yasser M. Sanad, Jing Han and Steven L. Foley

    Citation: BMC Microbiology 2020 20:353

    Content type: Review

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  33. The use of animal models with depleted intestinal microbiota has recently increased thanks to the huge interest in the potential role of these micro-organisms in human health. In particular, depletion of gut b...

    Authors: Pauline Tirelle, Jonathan Breton, Gaëtan Riou, Pierre Déchelotte, Moïse Coëffier and David Ribet

    Citation: BMC Microbiology 2020 20:340

    Content type: Research article

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  34. The long-held notion that, without urinary tract or circulatory infection, bladder urine and blood are sterile biofluids has been disproven. There have been no previous reports on the kidney pelvis urinary mic...

    Authors: Fengping Liu, Nan Zhang, Yunhong Wu, Peng Jiang, Tingting Jiang, Yang Wang, Yuwei Zhang, Qixiao Zhai, Yeqing Zou and Ninghan Feng

    Citation: BMC Microbiology 2020 20:336

    Content type: Research article

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  35. Microencapsulated organic acids and botanicals have the potential to develop into important tools for the poultry industry. A blend of organic acids and botanicals (AviPlus®P) has previously shown to reduce Salmo...

    Authors: Kristina M. Feye, Christina L. Swaggerty, Michael H. Kogut, Steven C. Ricke, Andrea Piva and Ester Grilli

    Citation: BMC Microbiology 2020 20:332

    Content type: Research article

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  36. The fungal communities inhabiting natural Ophiocordyceps sinensis play critical ecological roles in alpine meadow ecosystem, contribute to infect host insect, influence the occurrence of O. sinensis, and are repe...

    Authors: Chuan-Bo Zhang, Chao-Hui Ren, Yan-Li Wang, Qi-Qi Wang, Yun-Sheng Wang and Qing-Bei Weng

    Citation: BMC Microbiology 2020 20:331

    Content type: Research article

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  37. Yaks are able to utilize the gastrointestinal microbiota to digest plant materials. Although the cellulolytic bacteria in the yak rumen have been reported, there is still limited information on the diversity o...

    Authors: Ga Gong, Saisai Zhou, Runbo Luo, Zhuoma Gesang and Sizhu Suolang

    Citation: BMC Microbiology 2020 20:302

    Content type: Research article

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  38. Neuropathic pain is an abnormally increased sensitivity to pain, especially from mechanical or thermal stimuli. To date, the current pharmacological treatments for neuropathic pain are still unsatisfactory. Th...

    Authors: Guo-Jie Brandon-Mong, Grace Tzun-Wen Shaw, Wei-Hsin Chen, Chien-Chang Chen and Daryi Wang

    Citation: BMC Microbiology 2020 20:295

    Content type: Research article

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    The Correction to this article has been published in BMC Microbiology 2020 20:377

  39. Dental implants have become well-established in oral rehabilitation for fully or partially edentulous patients. However, peri-implantitis often leads to the failure of dental implants. The aim of this study wa...

    Authors: Shichong Qiao, Dongle Wu, Mengge Wang, Shujiao Qian, Yu Zhu, Junyu Shi, Yongjun Wei and Hongchang Lai

    Citation: BMC Microbiology 2020 20:293

    Content type: Research article

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  40. In recent years, the microbiome field has undergone a shift from clustering-based methods of operational taxonomic unit (OTU) designation based on sequence similarity to denoising algorithms that identify exac...

    Authors: Shirin Moossavi, Faisal Atakora, Kelsey Fehr and Ehsan Khafipour

    Citation: BMC Microbiology 2020 20:290

    Content type: Research article

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  41. The experimental materials were a 60-year-old tea tree (Camellia sinensis cv. Shu Cha Zao; SCZ) (the mother plant) and 1-year-old and 20-year-old plants of SCZ that originated as mother plant cuttings. The aim of...

    Authors: Zhenzhen Wu, Qingqing Su, Yuchen Cui, Hongzhu He, Jiali Wang, Yong Zhang, Yu Zhao, Hassan Abul, Yunqiu Yang and Yanhua Long

    Citation: BMC Microbiology 2020 20:270

    Content type: Research article

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  42. Tor putitora, the largest freshwater fish of the Indian subcontinent, is an endangered species. Several factors have been attributed towards its continuous population decrease, but very little is known about the ...

    Authors: Himani Khurana, Durgesh Narain Singh, Anoop Singh, Yogendra Singh, Rup Lal and Ram Krishan Negi

    Citation: BMC Microbiology 2020 20:249

    Content type: Research article

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  43. The Qinghai-Tibetan Plateau represents one of the most important component of the terrestrial ecosystem and a particularly vulnerable region, which harbouring complex and diverse microbiota. The knowledge abou...

    Authors: Mengjun Zhang, Liwei Chai, Muke Huang, Weiqian Jia, Jiabao Guo and Yi Huang

    Citation: BMC Microbiology 2020 20:235

    Content type: Research article

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  44. Primary ovarian failure (POF) is defined as follicular failure in women of reproductive age. Although many factors are speculated to contribute to the occurrence of POF, the exact aetiology remains unclear. Mo...

    Authors: Juan Wang, Jieying Xu, Qixin Han, Weiwei Chu, Gang Lu, Wai-Yee Chan, Yingying Qin and Yanzhi Du

    Citation: BMC Microbiology 2020 20:230

    Content type: Research article

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  45. Gut microbiota plays an important role in physiological and pathological processes of the host organism, including aging. Microbiota composition was shown to vary significantly throughout the life course. Age-...

    Authors: Alexander Vaiserman, Mariana Romanenko, Liubov Piven, Vladislav Moseiko, Oleh Lushchak, Nadiia Kryzhanovska, Vitaly Guryanov and Alexander Koliada

    Citation: BMC Microbiology 2020 20:221

    Content type: Research article

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