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Microbiome dynamics in human diseases

Guest Editors:
Animesh Acharjee: Institute of Cancer and Genomic Sciences, University of Birmingham, UK
Mangesh Suryavanshi: Lerner Research Institute, Cleveland Clinic, USA



The ‘human microbiome’ comprises the complex and diverse, microbial ecosystems that colonize different organs and tissues of the human bodies. The human microbiota consists of bacteria, archaea, viruses as well as eukaryotes (e.g. fungi and protozoa), which significantly impact the physiology, homeostasis and overall health of the human body. Since the microbiome is a complex and variable microbial community that responds to multiple factors, our current understanding of the microbiota dynamics and impact on disease development remains incomplete.

BMC Microbiology presents the collection `Microbiome dynamics in human diseases´ which comprises research and methods addressing the complex role of the human microbiome, especially in the context of human diseases and biological dysfunctions. By acknowledging that ‘human microbiome research’ is rapidly evolving and fundamentally changing the way we study and treat human diseases, the overall goal of the collection has been to enhance our knowledge on microbiome diversity and functions, microbiome-host interactions, and the role of microbiomes in health and disease.

Meet the Guest Editors

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Animesh Acharjee: Institute of Cancer and Genomic Sciences, University of Birmingham, UK

Dr Acharjee is an Assistant Professor of Integrative Analytics and AI (Health Data Science) at the University of Birmingham. He is also the Deputy Program Director for the MSc - Health Data Science program in Dubai. He has degrees in Electrical Engineering, Bioinformatics, and an applied PhD in Statistical Machine Learning. He has worked as a systems biologist, biostatistician and research scientist focusing on multi-modal and multi-omics data analytics. With expertise in translational medicine, he has collaborated with prestigious institutions and published extensively. His research interests include workflow for microbiome, integrative data analysis, predictive biomarker discovery, and bioinformatics methods for diagnostics.

Mangesh Suryavanshi: Lerner Research Institute, Cleveland Clinic, USA

Dr Mangesh Suryavanshi is a researcher with a robust academic background in microbiology, especially focusing on gut microbiome studies. He has completed his PhD with the support of a Council of Scientific and Industrial Research (CSIR) Fellowship. He further enhanced his research skills as a postdoctoral researcher at the Department of Science and Technology (DST) SERB-NPDF (India). In 2021, he joined the research team at Cleveland Clinic (USA) where he currently focuses on microbiome science related to metabolic diseases. His main research areas include studying the impact of oxalic acid on the gut-kidney axis and cardiovascular disease events and investigating antimicrobial genes from the urinary microbiome for urinary health prospects. 

About the collection

The `human microbiome’ comprises the complex and diverse, microbial ecosystems that colonize different organs and tissues of the human bodies. The human microbiota consists of bacteria, archaea, viruses as well as eukaryotes (e.g. fungi and protozoa), which significantly impact the physiology, homeostasis and overall health of the human body. While the gut microbiome is certainly the most studied human microbial community, knowledge for instance on the lung, oral, skin and vaginal microbiomes is also increasing.

The human microbiome contributes to the regulation of several metabolic functions, trains and develops major components of the innate and adaptive immune system, and protects against pathogens. However, the alteration of the microbiota composition and functions, in addition to genetic risks, has been associated with various systemic and chronic diseases, including neurological, cardiovascular, gastrointestinal, metabolic, respiratory and allergic diseases, as well as cancer. As many studies are finding increasing evidence of important and complex relationships between the human microbiome and diseases, considerable efforts have been made over the past decade to better understand the microbiome–host mechanisms of interactions, as well as how diseases caused by a ‘dysfunctional microbiome’ develop and can be treated. Nonetheless, because the microbiome is a complex and variable microbial community that responds to multiple factors, our current understanding of the microbiota dynamics and impact on disease development remains incomplete.

In support of The United Nation’s Sustainable Development Goals 3 (SDG3), ‘Good health and well-being’, which aims to ‘Ensure healthy lives and promote well-being for all at all ages’, BMC Microbiology published the collection ‘Microbiome dynamics in human diseases’. It highlights research and methods addressing the complex role of the human microbiome, especially in the context of human diseases and biological dysfunctions. By acknowledging that ‘human microbiome research’ is rapidly evolving and fundamentally changing the way we study and treat human diseases, the overall goal of the collection has been to enhance our knowledge on microbiome diversity and functions, microbiome-host interactions and the role of microbiomes in health and disease.

Our collection aims to showcase recent research covering a broad range of topics including, but not limited to:

  • Microbiota eubiosis and dysbiosis
  • Progress in microbiome-based therapeutics
  • Application of ecological principles, biostatistical analysis and machine learning for microbiome-based therapeutics
  • Personalized microbiome dynamics
  • Mechanistic understanding on how the metabolic environment shapes the microbiome composition and function, and how microbial metabolites affect the host
  • Understanding the role and implications of the microbiota gut–brain axis in health and disease
  • Host-microbiome interactions and host-environment-microbiome interactions
  • Multi-omics and multi-modal technologies applied and integrated to study the microbiome dynamics, the microbiome-disease relationship, and the response to drugs and potential treatments
  • Machine learning and artificial intelligence-based computational approaches and models for the analysis of microbiome data and the microbiome-disease relationship
  • Computational workflows or pipelines for microbiome analysis 
  • The diagnostic and prognostic potential of microbiome-based biomarkers in disease
  • Microbiome-based novel interventions (e.g. supplementation with prebiotics and probiotics, fecal microbiota transplantation (FMT), dietary changes)
  • Diet and its effects on gut microbiome biodiversity and function
  • Longitudinal microbiome data analysis

Image credit: Springer Nature

  1. Severe burns may alter the stability of the intestinal flora and affect the patient’s recovery process. Understanding the characteristics of the gut microbiota in the acute phase of burns and their association...

    Authors: Bochen Hou, Honglan Zhang, Lina Zhou, Biao Hu, Wenyi Tang, Bo Ye, Cui Wang, Yongmei Xu, Lingyun Zou and Jun Hu
    Citation: BMC Microbiology 2024 24:124
  2. Primary nephrotic syndrome (PNS) is a common glomerular disease in children. Clostridium butyricum (C. butyricum), a probiotic producing butyric acid, exerts effective in regulating inflammation. This study was d...

    Authors: Ting Li, Xiaolong Ma, Ting Wang, Wenyan Tian, Jian Liu, Wenke Shen, Yuanyuan Liu, Yiwei Li, Xiaoxu Zhang, Junbai Ma, Xiaoxia Zhang, Jinhai Ma and Hao Wang
    Citation: BMC Microbiology 2024 24:97
  3. Cervicovaginal microbiome plays an important role in the persistence of HPV infection and subsequent disease development. However, cervicovaginal microbiota varied cross populations with different habits and r...

    Authors: Yao Zhang, Xu Wu, Dan Li, Rong Huang, Xiangyu Deng, Mingxing Li, Fukuan Du, Yueshui Zhao, Jing Shen, Yu Chen, Pingxiu Zhang, Congcui Hu, Zhangang Xiao and Qinglian Wen
    Citation: BMC Microbiology 2024 24:94
  4. Probiotics are a potentially effective therapy for inflammatory bowel disease (IBD); IBD is linked to impaired gut microbiota and intestinal immunity. However, the utilization of an antibiotic cocktail (Abx) p...

    Authors: Jing Xu, Haoming Xu, Xue Guo, Hailan Zhao, Jiaqi Wang, Jianhong Li, Jie He, Hongli Huang, Chen Huang, Chong Zhao, Yingfei Li, Youlian Zhou, Yao Peng and Yuqiang Nie
    Citation: BMC Microbiology 2024 24:91
  5. Extrauterine growth restriction (EUGR) represents a prevalent condition observed in preterm neonates, which poses potential adverse implications for both neonatal development and long-term health outcomes. The...

    Authors: Yumei Liang, Xiaomin Yao, Zida Meng, Jinyun Lan, Yanqing Qiu, Chao Cen and Yanni Feng
    Citation: BMC Microbiology 2024 24:82
  6. To explore the changes and potential mechanisms of microbiome in different parts of the upper airway in the development of pediatric OSA and observe the impact of surgical intervention on oral microbiome for p...

    Authors: Lucheng Fang, Aikebaier Tuohuti, Wanyue Cai and Xiong Chen
    Citation: BMC Microbiology 2024 24:79
  7. Perioperative neurocognitive dysfunction (PND) emerges as a common postoperative complication among elderly patients. Currently, the mechanism of PND remains unclear, but there exists a tendency to believe tha...

    Authors: Yanfang Yang, Na Li, Yubo Gao, Fanning Xu, Hui Chen, Chun Zhang and Xinli Ni
    Citation: BMC Microbiology 2024 24:70
  8. In the current study, for the first time, we reported a novel HCV molecular diagnostic approach termed reverse transcription loop-mediated isothermal amplification integrated with a gold nanoparticles-based la...

    Authors: Yuanfang Shi, Qingxue Zhou, Shilei Dong, Qi Zhao, Xue Wu, Peng Yang, Xiaoyan Zeng, Xinggui Yang, Yan Tan, Xinhua Luo, Zhenghua Xiao and Xu Chen
    Citation: BMC Microbiology 2024 24:68
  9. Pediatric chronic intestinal pseudo-obstruction (PIPO) is a rare disease characterized by symptoms and radiological signs suggestive of intestinal obstruction, in the absence of lumen-occluding lesions. It res...

    Authors: Giulia Radocchia, Massimiliano Marazzato, Karim Ben Harbi, Elena Capuzzo, Fabrizio Pantanella, Roberto De Giorgio, Matteo Guarino, Anna Costanzini, Letizia Zenzeri, Pasquale Parisi, Alessandro Ferretti, Enrico Felici, Anna Teresa Palamara, Giovanni Di Nardo and Serena Schippa
    Citation: BMC Microbiology 2024 24:48
  10. Sepsis can cause immune dysregulation and multiple organ failure in patients and eventually lead to death. The gut microbiota has demonstrated its precise therapeutic potential in the treatment of various dise...

    Authors: Feiyu Luan, Yang Zhou, Xiaohui Ma, Yue Li, Yahui Peng, Xiaonan Jia, Nana Li, Xibo Wang, Yinghao Luo, Mingyin Man, Qianqian Zhang, Chunying Wang, Kaijiang Yu, Mingyan Zhao and Changsong Wang
    Citation: BMC Microbiology 2024 24:45
  11. COVID-19 emerged in late 2019 and has occasioned more than 765 millions cumulative cases and 6.9 millions of deaths globally. Notably, around 70% of patients with severe COVID-19 are men. Therefore, it is to b...

    Authors: Rubén Alberto Bayardo-González, Marcela Peña-Rodríguez, Ana Laura Pereira-Suárez, Alina Xcaret Rubio-Sánchez, Mariel García-Chagollán, Daniel Natividad Valenzuela-Orozco, Melida del Rosario Lizarazo-Taborda, Jesús Mora-Mora and Natali Vega-Magaña
    Citation: BMC Microbiology 2024 24:32
  12. Colorectal cancer (CRC) is a prevalent malignant malignancy affecting the gastrointestinal tract that is usually treated clinically with chemotherapeutic agents, whereas chemotherapeutic agents can cause sever...

    Authors: Fenfang Yue, Xiangdi Zeng, Yufan Wang, Yilin Fang, Mengyun Yue, Xuanqi Zhao, Ruizhe Zhu, Qingwei Zeng, Jing Wei and Tingtao Chen
    Citation: BMC Microbiology 2024 24:8
  13. People living with HIV (PLWH) with chronic inflammation may have an increasing risk for coronavirus disease 2019 (COVID-19) severity; however, the impact of their gut microbiota on COVID-19 is not fully elucid...

    Authors: Aya Ishizaka, Michiko Koga, Taketoshi Mizutani, Seiya Yamayoshi, Kiyoko Iwatsuki-Horimoto, Eisuke Adachi, Yutaka Suzuki, Yoshihiro Kawaoka and Hiroshi Yotsuyanagi
    Citation: BMC Microbiology 2024 24:6
  14. Intrinsic metabolism shapes the immune environment associated with immune suppression and tolerance in settings such as organ transplantation and cancer. However, little is known about the metabolic activities...

    Authors: Bing Ma, Samuel J. Gavzy, Michael France, Yang Song, Hnin Wai Lwin, Allison Kensiski, Vikas Saxena, Wenji Piao, Ram Lakhan, Jegan Iyyathurai, Lushen Li, Christina Paluskievicz, Long Wu, Marina WillsonShirkey, Emmanuel F. Mongodin, Valeria R. Mas…
    Citation: BMC Microbiology 2023 23:394
  15. Depression and anxiety are common comorbid diseases of constipation. Fecal microbiota transplantation (FMT) significantly relieves gastrointestinal-related symptoms, but its impact on psychiatric symptoms rema...

    Authors: Chuanli Yang, Tianjiao Hu, Xin Xue, Xiaohu Su, Xuan Zhang, Yunhe Fan, Xiaobing Shen and Xiushan Dong
    Citation: BMC Microbiology 2023 23:389
  16. The goal of this study was to comprehensively investigate the characteristics of gut microbiota dysbiosis and metabolites levels in very low or extremely low birth weight (VLBW/ELBW) infants with white matter ...

    Authors: Ling Liu, Min Xiang, Xiangsheng Cai, Benqing Wu, Chaohong Chen, Nali Cai and Dang Ao
    Citation: BMC Microbiology 2023 23:387
  17. Peutz–Jeghers Syndromeis a rare autosomal dominant genetic disease characterized by gastrointestinal hamartomatous polyps and skin and mucous membrane pigmentation. The pathogenesis of PJS remains unclear; how...

    Authors: An Zhou, Bo Tang, Yuhong Xie, Shengpeng Li, Xu Xiao, Lingyi Wu, Dianji Tu, Sumin Wang, Yunxuan Feng, Xiaojie Feng, Yi Lai, Shoubin Ning and Shiming Yang
    Citation: BMC Microbiology 2023 23:373
  18. Coronary artery disease (CAD) is a widespread heart condition caused by atherosclerosis and influences millions of people worldwide. Early detection of CAD is challenging due to the lack of specific biomarkers...

    Authors: Liuying Chen, Xuanting Mou, Jingjing Li, Miaofu Li, Caijie Ye, Xiaofei Gao, Xiaohua Liu, Yunlong Ma, Yizhou Xu and Yigang Zhong
    Citation: BMC Microbiology 2023 23:320
  19. Traditionally, conventional microbiological culture methods have been used to detect pathogenic microorganisms in chronic osteomyelitis. However, these methods have been found to have a low detection rate, com...

    Authors: Kang Zhang, Yu-zhe Bai, Chang Liu, Shan-shan Liu, Xin-xin Lu and Run-gong Yang
    Citation: BMC Microbiology 2023 23:313
  20. Tobramycin inhalation solution (TIS) and chronic azithromycin (AZ) have known clinical benefits for children with CF, likely due to antimicrobial and anti-inflammatory activity. The effects of chronic AZ in co...

    Authors: Brandie D. Wagner, Edith T. Zemanick, Scott D. Sagel, Charles E. Robertson, Mark J. Stevens, Nicole Mayer-Hamblett, George Retsch-Bogart, Bonnie W. Ramsey and J. Kirk Harris
    Citation: BMC Microbiology 2023 23:312