2018 Vol. 9, No. 5

Say bye to crude FMT by targeting purified microbial cells
from donated healthy stool using an automatic purification
system. Scanning electron microscope confirmed the “clean”
bacteria from the frozen fecal microbiota suspension which
was provided by fmtBank as a national non-profit stool
Microbes and host dance in harmony or disarray?
Zhihua Liu
2018, 9(5): 395-396. doi: 10.1007/s13238-018-0545-4
Insights into the role of gut microbiota in obesity: pathogenesis, mechanisms, and therapeutic perspectives
Lijuan Sun, Lanjing Ma, Yubo Ma, Faming Zhang, Changhai Zhao, Yongzhan Nie
2018, 9(5): 397-403. doi: 10.1007/s13238-018-0546-3
Help, hope and hype: ethical considerations of human microbiome research and applications
Yonghui Ma, Hua Chen, Canhui Lan, Jianlin Ren
2018, 9(5): 404-415. doi: 10.1007/s13238-018-0537-4
Gut microbiota derived metabolites in cardiovascular health and disease
Zeneng Wang, Yongzhong Zhao
2018, 9(5): 416-431. doi: 10.1007/s13238-018-0549-0
Trillions of microbes inhabit the human gut, not only providing nutrients and energy to the host from the ingested food, but also producing metabolic bioactive signaling molecules to maintain health and elicit disease, such as cardiovascular disease (CVD). CVD is the leading cause of mortality worldwide. In this review, we presented gut microbiota derived metabolites involved in cardiovascular health and disease, including trimethylamine-N-oxide (TMAO), uremic toxins, short chain fatty acids (SCFAs), phytoestrogens, anthocyanins, bile acids and lipopolysaccharide. These gut microbiota derived metabolites play critical roles in maintaining a healthy cardiovascular function, and if dysregulated, potentially causally linked to CVD. A better understanding of the function and dynamics of gut microbiota derived metabolites holds great promise toward mechanistic predicative CVD biomarker discoveries and precise interventions.
Pharmacomicrobiomics: a novel route towards personalized medicine?
Marwah Doestzada, Arnau Vich Vila, Alexandra Zhernakova, Debby P. Y. Koonen, Rinse K. Weersma, Daan J. Touw, Folkert Kuipers, Cisca Wijmenga, Jingyuan Fu
2018, 9(5): 432-445. doi: 10.1007/s13238-018-0547-2
Inter-individual heterogeneity in drug response is a serious problem that affects the patient's wellbeing and poses enormous clinical and financial burdens on a societal level. Pharmacogenomics has been at the forefront of research into the impact of individual genetic background on drug response variability or drug toxicity, and recently the gut microbiome, which has also been called the second genome, has been recognized as an important player in this respect. Moreover, the microbiome is a very attractive target for improving drug efficacy and safety due to the opportunities to manipulate its composition. Pharmacomicrobiomics is an emerging field that investigates the interplay of microbiome variation and drugs response and disposition (absorption, distribution, metabolism and excretion). In this review, we provide a historical overview and examine current state-of-the-art knowledge on the complex interactions between gut microbiome, host and drugs. We argue that combining pharmacogenomics and pharmacomicrobiomics will provide an important foundation for making major advances in personalized medicine.
Of genes and microbes: solving the intricacies in host genomes
Jun Wang, Liang Chen, Na Zhao, Xizhan Xu, Yakun Xu, Baoli Zhu
2018, 9(5): 446-461. doi: 10.1007/s13238-018-0532-9
Microbiome research is a quickly developing field in biomedical research, and we have witnessed its potential in understanding the physiology, metabolism and immunology, its critical role in understanding the health and disease of the host, and its vast capacity in disease prediction, intervention and treatment. However, many of the fundamental questions still need to be addressed, including the shaping forces of microbial diversity between individuals and across time. Microbiome research falls into the classical nature vs. nurture scenario, such that host genetics shape part of the microbiome, while environmental influences change the original course of microbiome development. In this review, we focus on the nature, i.e., the genetic part of the equation, and summarize the recent efforts in understanding which parts of the genome, especially the human and mouse genome, play important roles in determining the composition and functions of microbial communities, primarily in the gut but also on the skin. We aim to present an overview of different approaches in studying the intricate relationships between host genetic variations and microbes, its underlying philosophy and methodology, and we aim to highlight a few key discoveries along this exploration, as well as current pitfalls. More evidence and results will surely appear in upcoming studies, and the accumulating knowledge will lead to a deeper understanding of what we could finally term a "hologenome", that is, the organized, closely interacting genome of the host and the microbiome.
Microbiota transplantation: concept, methodology and strategy for its modernization
Faming Zhang, Bota Cui, Xingxiang He, Yuqiang Nie, Kaichun Wu, Daiming Fan, Study Group FMT-standardization
2018, 9(5): 462-473. doi: 10.1007/s13238-018-0541-8
Fecal microbiota transplantation (FMT) has become a research focus of biomedicine and clinical medicine in recent years. The clinical response from FMT for different diseases provided evidence for microbiota-host interactions associated with various disorders, including Clostridium difficile infection, inflammatory bowel disease, diabetes mellitus, cancer, liver cirrhosis, gutbrain disease and others. To discuss the experiences of using microbes to treat human diseases from ancient China to current era should be important in moving standardized FMT forward and achieving a better future. Here, we review the changing concept of microbiota transplantation from FMT to selective microbiota transplantation, methodology development of FMT and stepup FMT strategy based on literature and state experts' perspectives.
The association of diet, gut microbiota and colorectal cancer: what we eat may imply what we get
Jia Yang, Jun Yu
2018, 9(5): 474-487. doi: 10.1007/s13238-018-0543-6
Despite the success of colonoscopy screening and recent advances in cancer treatment, colorectal cancer (CRC) still remains one of the most commonly diagnosed and deadly cancers, with a significantly increased incidence in developing countries where people are adapting to Western lifestyle. Diet has an important impact on risk of CRC. Multiple epidemiological studies have suggested that excessive animal protein and fat intake, especially red meat and processed meat, could increase the risk of developing CRC while fiber could protect against colorectal tumorigenesis. Mechanisms have been investigated by animal studies. Diet could re-shape the community structure of gut microbiota and influence its function by modulating the production of metabolites. Butyrate, one of the short-chain fatty acids (SCFAs), which act as a favorable source for colonocytes, could protect colonic epithelial cells from tumorigenesis via anti-inflammatory and antineoplastic properties through cell metabolism, microbiota homeostasis, antiproliferative, immunomodulatory and genetic/epigenetic regulation ways. In contrast, protein fermentation and bile acid deconjugation, which cause damage to colonic cells through proinflammatory and proneoplastic ways, lead to increased riskofdevelopingCRC.Inconclusion,abalanced diet with an increased abundance of fiber should be adopted to reduce the risk and prevent CRC.
Oral microbiomes: more and more importance in oral cavity and whole body
Lu Gao, Tiansong Xu, Gang Huang, Song Jiang, Yan Gu, Feng Chen
2018, 9(5): 488-500. doi: 10.1007/s13238-018-0548-1
Microbes appear in every corner of human life, and microbes affect every aspect of human life. The human oral cavity contains a number of different habitats. Synergy and interaction of variable oral microorganisms help human body against invasion of undesirable stimulation outside. However, imbalance of microbial flora contributes to oral diseases and systemic diseases. Oral microbiomes play an important role in the human microbial community and human health. The use of recently developed molecular methods has greatly expanded our knowledge of the composition and function of the oral microbiome in health and disease. Studies in oral microbiomes and their interactions with microbiomes in variable body sites and variable health condition are critical in our cognition of our body and how to make effect on human health improvement.
Single-cell metagenomics: challenges and applications
Yuan Xu, Fangqing Zhao
2018, 9(5): 501-510. doi: 10.1007/s13238-018-0544-5
With the development of high throughput sequencing and single-cell genomics technologies, many uncultured bacterial communities have been dissected by combining these two techniques. Especially, by simultaneously leveraging of single-cell genomics and metagenomics, researchers can greatly improve the efficiency and accuracy of obtaining whole genome information from complex microbial communities, which not only allow us to identify microbes but also link function to species, identify subspecies variations, study host-virus interactions and etc. Here, we review recent developments and the challenges need to be addressed in single-cell metagenomics, including potential contamination, uneven sequence coverage, sequence chimera, genome assembly and annotation. With the development of sequencing and computational methods, single-cell metagenomics will undoubtedly broaden its application in various microbiome studies.