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  1. An amendment to this paper has been published and can be accessed via the original article.

    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 21:293

    Content type: Correction

    Published on:

    The original article was published in BMC Microbiology 2021 21:181

  2. Graph-based analysis (GBA) of genome-scale metabolic networks has revealed system-level structures such as the bow-tie connectivity that describes the overall mass flow in a network. However, many pathways obt...

    Authors: Yajie Gao, Qianqian Yuan, Zhitao Mao, Hao Liu and Hongwu Ma

    Citation: BMC Microbiology 2021 21:292

    Content type: Research

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  3. Phytopathogenic bacteria are economically important because they affect crop yields and threaten the livelihoods of farmers worldwide. The genus Xanthomonas is particularly significant because it is associated wi...

    Authors: Ritah Nakayinga, Angela Makumi, Venansio Tumuhaise and William Tinzaara

    Citation: BMC Microbiology 2021 21:291

    Content type: Review

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  4. Poultry is the major reservoir of Campylobacter that contributes to human campylobacteriosis and threatens food safety. Litter contact has been linked to Campylobacter colonization, but the gut microecological im...

    Authors: Wei Yan, Qianqian Zhou, Zhongyang Yuan, Liang Fu, Chaoliang Wen, Ning Yang and Congjiao Sun

    Citation: BMC Microbiology 2021 21:290

    Content type: Research

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  5. Seed sanitization via chemical processes removes/reduces microbes from the external surfaces of the seed and thereby could have an impact on the plants’ health or productivity. To determine the impact of seed ...

    Authors: Anirudha R. Dixit, Christina L. M. Khodadad, Mary E. Hummerick, Cory J. Spern, LaShelle E. Spencer, Jason A. Fischer, Aaron B. Curry, Jennifer L. Gooden, Gretchen J. Maldonado Vazquez, Raymond M. Wheeler, Gioia D. Massa and Matthew W. Romeyn

    Citation: BMC Microbiology 2021 21:289

    Content type: Research

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  6. Extremophiles have attracted much attention in the last few decades, as they possess different properties by producing certain useful metabolites. However, the secondary metabolism of the extremophiles of Anta...

    Authors: Yuanyuan Wang, Lingbo Ma, Jian He, Zixuan Liu, Shaoping Weng, Lumin Wang, Jianguo He and Changjun Guo

    Citation: BMC Microbiology 2021 21:288

    Content type: Research

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  7. In Ethiopia, the distribution of bovine tuberculosis (BTB) has long been known and documented as a major problem of animal health. However, the burden of circulating M. bovis strains is poorly understood in the c...

    Authors: Mebrat Ejo, Belete Haile, Tsegaye Tariku, Seleshe Nigatu, Elias Kebede, Abebe Belete Bitew, Yitayew Demessie, Gashaw Getaneh, Atnaf Alebie, Musse Girma, Fusao Ota and Anwar Nuru

    Citation: BMC Microbiology 2021 21:286

    Content type: Research

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  8. Blastocystis sp. is an anaerobic intestinal protozoan parasite of humans and a wide range of animals worldwide. In the current study the correlation between the cysteine protease activity of clinical samples of

    Authors: Seyed Ahmad Karamati, Hamed Mirjalali, Maryam Niyyati, Abbas Yadegar, Hamid Asadzadeh Aghdaei, Ali Haghighi and Seyyed Javad Seyyed Tabaei

    Citation: BMC Microbiology 2021 21:285

    Content type: Research

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  9. Enterohemorrhagic Escherichia coli (EHEC) are responsible for severe diseases in humans, and the ruminant digestive tract is considered as their main reservoir. Their excretion in bovine feces leads to the contam...

    Authors: Audrey Segura, Yolande Bertin, Alexandra Durand, Mhammed Benbakkar and Evelyne Forano

    Citation: BMC Microbiology 2021 21:284

    Content type: Research

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  10. The most common clinical manifestations of Staphylococcus aureus strains in the community are skin and soft-tissue infections. S. aureus could colonize the body sites and complicate the pathogenesis of skin disea...

    Authors: Haniyeh Khalili, Shahin Najar-Peerayeh, Mona Mahrooghi, Parvin Mansouri and Bita Bakhshi

    Citation: BMC Microbiology 2021 21:282

    Content type: Research

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  11. Bloodstream infection (BSI) caused by Staphylococcus aureus (S. aureus) can be life-threatening and pose a great challenge to infection control and clinical treatment. However, little information exists regarding...

    Authors: Xuezhi Wang, Dongzi Lin, Zengqi Huang, Jinmei Zhang, Wenyan Xie, Pen Liu, Huaiqi Jing and Jiazheng Wang

    Citation: BMC Microbiology 2021 21:281

    Content type: Research

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  12. Dextran sulfate sodium (DSS) replicates ulcerative colitis (UC)-like colitis in murine models. However, the microbial characteristics of DSS-triggered colitis require further clarification. To analyze the chan...

    Authors: Hao-Ming Xu, Hong-Li Huang, Yan-Di Liu, Jia-Qi Zhu, You-Lian Zhou, Hui-Ting Chen, Jing Xu, Hai-Lan Zhao, Xue Guo, Wei Shi, Yu-Qiang Nie and Yong-Jian Zhou

    Citation: BMC Microbiology 2021 21:279

    Content type: Research

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  13. Genomics-driven discoveries of microbial species have provided extraordinary insights into the biodiversity of human microbiota. In addition, a significant portion of genetic variation between microbiota exist...

    Authors: Elizabeth Fleming, Victor Pabst, Zoe Scholar, Ruoyun Xiong, Anita Y. Voigt, Wei Zhou, Amelia Hoyt, Rachel Hardy, Anna Peterson, Ryan Beach, Yvette Ondouah-Nzutchi, Jinhong Dong, Lucinda Bateman, Suzanne D. Vernon and Julia Oh

    Citation: BMC Microbiology 2021 21:278

    Content type: Methodology article

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  14. Fusobacterium nucleatum (F. n) is an important opportunistic pathogen causing oral and gastrointestinal disease. Faecalibacterium prausnitzii (F. p) is a next-generation probiotic and could serve as a biomarker ...

    Authors: Lirong Bao, Cheng Zhang, Jinglu Lyu, Caixia Yan, Ranran Cao, Ming Pan and Yan Li

    Citation: BMC Microbiology 2021 21:277

    Content type: Research

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  15. Compared to the huge microbial diversity in most mammals, human gut microbiomes have lost diversity while becoming specialized for animal-based diets – especially compared to chimps, their genetically closest ...

    Authors: Louise B. Thingholm, Corinna Bang, Malte C. Rühlemann, Annika Starke, Florian Sicks, Verena Kaspari, Anabell Jandowsky, Kai Frölich, Gabriele Ismer, Andreas Bernhard, Claudia Bombis, Barbara Struve, Philipp Rausch and Andre Franke

    Citation: BMC Microbiology 2021 21:276

    Content type: Research

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  16. Fecal microbiota transplantation (FMT) in patients with ulcerative colitis has shown variable efficacy depending on the protocol used. A previous randomized controlled trial reported that anaerobic preparation...

    Authors: Hirotaka Shimizu, Katsuhiro Arai, Takashi Asahara, Takuya Takahashi, Hirokazu Tsuji, Satoshi Matsumoto, Ichiro Takeuchi, Reiko Kyodo and Yuichiro Yamashiro

    Citation: BMC Microbiology 2021 21:275

    Content type: Research

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  17. Chinese strong-flavor baijiu (CSFB), one of the three major baijiu types, is the most popular baijiu type among consumers in China. A variety of microbes are involved in metabolizing raw materials to produce e...

    Authors: Huanming Liu, Guangxun Tan, Qitong Chen, Weiwei Dong, Ping Chen, Kaiyun Cai, Yuanliang Hu, Weiyan Zhang, Nan Peng, Yunxiang Liang and Shumiao Zhao

    Citation: BMC Microbiology 2021 21:274

    Content type: Research

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  18. The aim of this study was to evaluate the anti-biofilm and anti-metabolic activities of zeolite-zinc oxide nanoparticles (Zeo/ZnONPs)-based antimicrobial photodynamic therapy (aPDT) against pre-formed polymicr...

    Authors: Maryam Pourhajibagher and Abbas Bahador

    Citation: BMC Microbiology 2021 21:273

    Content type: Research

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  19. In recent years, interest in the consumption of ready-to-eat (RTE) food products has been increased in many countries. However, RTE products particularly those prepared by meat may be potential vehicles of ant...

    Authors: Maryam Rajaei, Mir-Hassan Moosavy, Sahar Nouri Gharajalar and Seyed Amin Khatibi

    Citation: BMC Microbiology 2021 21:272

    Content type: Research

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  20. The purpose of the study was to investigate the effect of probiotics on biofilm acidogenicity and on the number of salivary Streptococcus mutans and lactobacilli in orthodontic patients.

    Authors: Sahal Alforaidi, Andrea Bresin, Naif Almosa, Anna Lehrkinder and Peter Lingström

    Citation: BMC Microbiology 2021 21:271

    Content type: Research

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  21. Rickettsia is the pathogen of Q fever, Brucella ovis is the pathogen of brucellosis, and both of them are Gram-negative bacteria which are parasitic in cells. The mixed infection of rickettsia and Brucella ovis ...

    Authors: Jiangqin Song, Xiaorong Hu, Xiaolong Li, Youping Chen, Xiangyuan Yan, Weifang Zhu, Yan Ding and Junyang Zhou

    Citation: BMC Microbiology 2021 21:270

    Content type: Research

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  22. Infection in patients with acute pancreatitis, especially severe acute pancreatitis patients, is a common and important phenomenon, and the distributions and drug resistance profiles of bacteria causing biliar...

    Authors: Shayan Chen, Jiyu Shi, Minghui Chen, Jun Ma, Zhaowei Zeng, Rui Wang, Yunfeng Cui and Xue Gao

    Citation: BMC Microbiology 2021 21:269

    Content type: Research

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  23. Auto-aggregation is a desired property for probiotic strains because it is suggested to promote colonization of the human intestine, to prevent pathogen infections and to modulate the colonic mucosa. We recent...

    Authors: Julia Isenring, Annelies Geirnaert, Christophe Lacroix and Marc J. A. Stevens

    Citation: BMC Microbiology 2021 21:268

    Content type: Research

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  24. Tuberculosis (TB) is a serious chronic infectious disease caused by Mycobacterium tuberculosis complex (MTBC). Hence, the development of a novel, simple, rapid and sensitive method to detect MTBC is of great sign...

    Authors: Junfei Huang, Ziyu Xiao, Xinggui Yang, Xu Chen, Xiaojuan Wang, Yijiang Chen, Wenlin Zheng, Wei Chen, Huijuan Chen and Shijun Li

    Citation: BMC Microbiology 2021 21:267

    Content type: Research

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  25. The anoxic redox control binary system plays an important role in the response to oxygen as a signal in the environment. In particular, phosphorylated ArcA, as a global transcription factor, binds to the promo...

    Authors: Junxiang Yan, Yuehua Li, Xueqian Guo, Xiaochen Wang, Fenxia Liu, Ang Li and Boyang Cao

    Citation: BMC Microbiology 2021 21:266

    Content type: Research

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  26. Preeclampsia (PE) is a condition of high blood pressure that is usually concurrent with proteinuria in pregnancy. PE complicates the management of both maternal and fetal health and contributes to most adverse...

    Authors: Lihui Huang, Min Cai, Li Li, Xin Zhang, Yang Xu, Jianhua Xiao, Qian Huang, Guijuan Luo, Zhaoyang Zeng, Cuiyuan Jin, Yuanxiang Jin, Jun He and Weitao Yang

    Citation: BMC Microbiology 2021 21:265

    Content type: Research

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  27. Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen for human infection. Hospital-acquired (HA) and community-acquired (CA) MRSA infections are serious clinical problems worldwide. In this...

    Authors: Feng Liao, Wenpeng Gu, Xiaoqing Fu, Bin Yuan and Yunhui Zhang

    Citation: BMC Microbiology 2021 21:264

    Content type: Research

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  28. Microbiome big data from population-scale cohorts holds the key to unleash the power of microbiomes to overcome critical challenges in disease control, treatment and precision medicine. However, variations int...

    Authors: Li Shao, Jie Liao, Jingyang Qian, Wenbin Chen and Xiaohui Fan

    Citation: BMC Microbiology 2021 21:263

    Content type: Database

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  29. This study aimed to determine the frequency of methicillin-resistant Staphylococcus aureus (MRSA), antibiotic resistance patterns, superantigenic toxins profile, and clonality of this pathogen in patients with ca...

    Authors: Effat Abbasi Montazeri, Azar Dokht Khosravi, Saeedeh Khazaei and Ali Sabbagh

    Citation: BMC Microbiology 2021 21:262

    Content type: Research

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  30. Prompt and accurate identification of carbapenemase production is essential for appropriate treatment and infection control. NG-Test Carba 5 (termed herein “Carba 5”; NG Biotech, Guipry, France) is a multiplex...

    Authors: Jung Yoon, Chang Hyun Kim, Soo-Young Yoon, Chae Seung Lim and Chang Kyu Lee

    Citation: BMC Microbiology 2021 21:260

    Content type: Research

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  31. Oral iron supplementation is commonly prescribed for anemia and may play an important role in the gut microbiota recovery of anemic individuals who received antibiotic treatment. This study aims to investigate...

    Authors: Thibault Cuisiniere, Annie Calvé, Gabriela Fragoso, Manon Oliero, Roy Hajjar, Emmanuel Gonzalez and Manuela M. Santos

    Citation: BMC Microbiology 2021 21:259

    Content type: Research

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  32. The Shiga toxin-producing Escherichia coli (STEC) represented a great risk to public health. In this study, 60 STEC strains recovered from broiler and duck fecal samples, cow’s milk, cattle beef, human urine, and...

    Authors: Mohamed Sabry Abd Elraheam Elsayed, Samah Mahmoud Eldsouky, Tamer Roshdy, Abeer Mohamed Ahmed Bayoume, Ghada M. Nasr, Ali S. A. Salama, Behiry A. Akl, Al Shaimaa Hasan, Amany Kasem Shahat, Rana Atef Khashaba, Walid Abdellatif Abdelhalim, Hend E. Nasr, Lina Abdelhady Mohammed and Ahmed Salah

    Citation: BMC Microbiology 2021 21:257

    Content type: Research

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  33. Microbial dysbiosis with increased Staphylococcus aureus (S. aureus) colonization on the skin is a hallmark of atopic dermatitis (AD), however most microbiome studies focus on bacteria in the flexures and the mic...

    Authors: Rie Dybboe Bjerre, Jacob Bak Holm, Albert Palleja, Julie Sølberg, Lone Skov and Jeanne Duus Johansen

    Citation: BMC Microbiology 2021 21:256

    Content type: Research

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  34. Biofilms disperse in response to specific environmental cues, such as reduced oxygen concentration, changes in nutrient concentration and exposure to nitric oxide. Interestingly, biofilms do not completely dis...

    Authors: Harikrishnan A. S. Nair, Sujatha Subramoni, Wee Han Poh, Nabilah Taqiah Binte Hasnuddin, Martin Tay, Michael Givskov, Tim Tolker-Nielsen, Staffan Kjelleberg, Diane McDougald and Scott A. Rice

    Citation: BMC Microbiology 2021 21:255

    Content type: Research

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  35. Cellulolytic microorganisms are considered a key player in the degradation of plant biomass in various environments. These microorganisms can be isolated from various environments, such as soils, the insect gu...

    Authors: Siham Fatani, Yoshimoto Saito, Mohammed Alarawi, Takashi Gojobori and Katsuhiko Mineta

    Citation: BMC Microbiology 2021 21:254

    Content type: Research

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  36. Long-term trends in freshwater bacterial community composition (BCC) and dynamics are not yet well characterized, particularly in large lake ecosystems. We addressed this gap by temporally (15 months) and spat...

    Authors: Abdolrazagh Hashemi Shahraki, Subba Rao Chaganti and Daniel Heath

    Citation: BMC Microbiology 2021 21:253

    Content type: Research article

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  37. This study was undertaken to discover whether the vaginal microbe of women at childbearing age is different among groups defined by urogenital tract infections, childbearing history and menstrual cycle, respec...

    Authors: Lijuan Cheng, Yan Gao, Qing Xia, Hui Wang, Xiuzhen Xie, Yurong Liu, Heying Shang and Yutao Diao

    Citation: BMC Microbiology 2021 21:252

    Content type: Research article

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  38. 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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  39. Probiotics are widely used in intestinal microbiota imbalance caused by sepsis, however, the protective mechanism is still unclear. This study aimed to explore protective effect of Lacticaseibacillus rhamnosus TR...

    Authors: Jiangtao Yin, Wen Sun, Xianqiang Yu, Xiaojia Xiao, Baiqiang Li, Zhihui Tong, Lu Ke, Wenjian Mao and Weiqin Li

    Citation: BMC Microbiology 2021 21:249

    Content type: Research

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  40. 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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  41. Saline and alkaline stresses damages the health of soil systems. Meanwhile, little is known about how saline or alkaline stress affects soil nitrifier and denitrifier communities. Therefore, we compared the re...

    Authors: Jiaxin Guo, Yongxue Zhou, Huijuan Guo and Wei Min

    Citation: BMC Microbiology 2021 21:246

    Content type: Research

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  42. Bacterial abortive infection (Abi) systems are type IV toxin–antitoxin (TA) system, which could elicit programmed cell death and constitute a native survival strategy of pathogenic bacteria under various stres...

    Authors: Xiaohong Chen, Aiqi Hu, Qian Zou, Sha Luo, Hetao Wu, Chunlan Yan, Tao Liu, Donglan He, Xiaohua Li and Guojun Cheng

    Citation: BMC Microbiology 2021 21:245

    Content type: Research

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