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[Online] Microecology

Guest Editors-in-Chief 
Li, Lanjuan, Zhejiang University, China
Weinstock,George, The Jackson Laboratory for Genomic Medicine, USA
Executive Associate Editors
Xiao,Yonghong, Zhejiang University, China
Xiang, Charlie, Zhejiang University, China
Liu, Liang, Macau University of Science and Technology, China
Proctor, Lita M., NIH Human Microbiome Project, USA
Knight, Rob, University of California, San Diego, USA
Shen, Zuyao, The Chinese University of Hong Kong, China
Vuitton, Dominique Angèle, Université de Franche-Comté, France
Wang, Hongyang , The Second Military Medical University, China
Wilmes, Paul, L’Université du Luxembourg, Luxembourg
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Engineering Solutions for Representative Models of the Gastrointestinal Human-Microbe Interface
Marc Mac Giolla Eain, Joanna Baginska, Kacy Greenhalgh, Joëlle V. Fritz, Frederic Zenhausern, Paul Wilmes
Engineering    2017, 3 (1): 60-65.
Abstract   HTML   PDF (1780KB)

Host-microbe interactions at the gastrointestinal interface have emerged as a key component in the governance of human health and disease. Advances in micro-physiological systems are providing researchers with unprecedented access and insights into this complex relationship. These systems combine the benefits of microengineering, microfluidics, and cell culture in a bid to recreate the environmental conditions prevalent in the human gut. Here we present the human-microbial cross talk (HuMiX) platform, one such system that leverages this multidisciplinary approach to provide a representative in vitro model of the human gastrointestinal interface. HuMiX presents a novel and robust means to study the molecular interactions at the host-microbe interface. We summarize our proof-of-concept results obtained using the platform and highlight its potential to greatly enhance our understanding of host-microbe interactions with a potential to greatly impact the pharmaceutical, food, nutrition, and healthcare industries in the future. A number of key questions and challenges facing these technologies are also discussed.

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The Gut Microbiota, Tumorigenesis, and Liver Diseases
Guishuai Lv, Ningtao Cheng, Hongyang Wang
Engineering    2017, 3 (1): 110-114.
Abstract   HTML   PDF (617KB)

In recent decades, diseases concerning the gut microbiota have presented some of the most serious public health problems worldwide. The human host’s physiological status is influenced by the intestinal microbiome, thus integrating external factors, such as diet, with genetic and immune signals. The notion that chronic inflammation drives carcinogenesis has been widely established for various tissues. It is surprising that the role of the microbiota in tumorigenesis has only recently been recognized, given that the presence of bacteria at tumor sites was first described more than a century ago. Extensive epidemiological studies have revealed that there is a strong link between the gut microbiota and some common cancers. However, the exact molecular mechanisms linking the gut microbiota and cancer are not yet fully understood. Changes to the gut microbiota are instrumental in determining the occurrence and progression of hepatocarcinoma, chronic liver diseases related to alcohol, nonalcoholic fatty liver disease (NAFLD), and cirrhosis. To be specific, the gut milieu may play an important role in systemic inflammation, endotoxemia, and vasodilation, which leads to complications such as spontaneous bacterial peritonitis and hepatic encephalopathy. Relevant animal studies involving gut microbiota manipulations, combined with observational studies on patients with NAFLD, have provided ample evidence pointing to the contribution of dysbiosis to the pathogenesis of NAFLD. Given the poor prognosis of these clinical events, their prevention and early management are essential. Studies of the composition and function of the gut microbiota could shed some light on understanding the prognosis because the microbiota serves as an essential component of the gut milieu that can impact the aforementioned clinical events. As far as disease management is concerned, probiotics may provide a novel direction for therapeutics for hepatocellular carcinoma (HCC) and NAFLD, given that probiotics function as a type of medicine that can improve human health by regulating the immune system. Here, we provide an overview of the relationships among the gut microbiota, tumors, and liver diseases. In addition, considering the significance of bacterial homeostasis, we discuss probiotics in this article in order to guide treatments for related diseases.

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Emerging Trends for Microbiome Analysis: From Single-Cell Functional Imaging to Microbiome Big Data
Jian Xu, Bo Ma, Xiaoquan Su, Shi Huang, Xin Xu, Xuedong Zhou, Wei Huang, Rob Knight
Engineering    2017, 3 (1): 66-70.
Abstract   HTML   PDF (813KB)

Method development has always been and will continue to be a core driving force of microbiome science. In this perspective, we argue that in the next decade, method development in microbiome analysis will be driven by three key changes in both ways of thinking and technological platforms: ① a shift from dissecting microbiota structureby sequencing to tracking microbiota state, function, and intercellular interaction via imaging; ② a shift from interrogating a consortium or population of cells to probing individual cells; and ③ a shift from microbiome data analysis to microbiome data science. Some of the recent method-development efforts by Chinese microbiome scientists and their international collaborators that underlie these technological trends are highlighted here. It is our belief that the China Microbiome Initiative has the opportunity to deliver outstanding “Made-in-China” tools to the international research community, by building an ambitious, competitive, and collaborative program at the forefront of method development for microbiome science.

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From Farming to Engineering: The Microbiota and Allergic Diseases
Dominique Angèle Vuitton, Jean-Charles Dalphin
Engineering    2017, 3 (1): 98-109.
Abstract   HTML   PDF (1056KB)

The steady increase of IgE-dependent allergic diseases after the Second World War is a unique phenomenon in the history of humankind. Numerous cross-sectional studies, comprehensive longitudinal cohort studies of children living in various types of environment, and mechanistic experimental studies have pointed to the disappearance of “protective factors” related to major changes in lifestyle and environment. A common unifying concept is that of the immunoregulatory role of the gut microbiota. This review focuses on the protection against allergic disorders that is provided by the farming environment and by exposure to microbial diversity. It also questions whether and how microbial bioengineering will be able in the future to restore an interplay that was beneficial to the proper immunological development of children in the past and that was irreversibly disrupted by changes in lifestyle. The protective “farming environment” includes independent and additional influences: contact with animals, stay in barns/stables, and consumption of unprocessed milk and milk products, by mothers during pregnancy and by children in early life. More than the overall quantity of microbes, the biodiversity of the farm microbial environment appears to be crucial for this protection, as does the biodiversity of the gut microbiota that it may provide. Use of conventional probiotics, especially various species or strains of Lactobacillus and Bifidobacterium, has not fulfilled the expectations of allergists and pediatricians to prevent allergy. Among the specific organisms present in cowsheds that could be used for prevention, Acinetobacter (A.) lwoffii F78, Lactococcus (L.) lactis G121, and Staphylococcus (S.) sciuri W620 seem to be the most promising, based on experimental studies in mouse models of allergic respiratory diseases. However, the development of a new generation of probiotics based on very productive research on the farming environment faces several obstacles that cannot be overcome without a close collaboration between microbiologists, immunologists, and bioengineers, as well as pediatricians, allergists, specialists of clinical trials, and ethical committees.

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The Composition of Colonic Commensal Bacteria According to Anatomical Localization in Colorectal Cancer
Liuyang Zhao, Xiang Zhang, Tao Zuo, Jun Yu
Engineering    2017, 3 (1): 90-97.
Abstract   HTML   PDF (1097KB)

Colorectal cancer (CRC) is a multistage disease resulting from complex factors, including genetic mutations, epigenetic changes, chronic inflammation, diet, and lifestyle. Recent accumulating evidence suggests that the gut microbiota is a new and important player in the development of CRC. Imbalance of the gut microbiota, especially dysregulated gut bacteria, contributes to colon cancer through mechanisms of inflammation, host defense modulations, oxidative stress, and alterations in bacterial-derived metabolism. Gut commensal bacteria are anatomically defined as four populations: luminal commensal bacteria, mucus-resident bacteria, epithelium-resident bacteria, and lymphoid tissue-resident commental bacteria. The bacterial flora that are harbored in the gastrointestinal (GI) tract vary both longitudinally and cross-sectionally by different anatomical localization. It is notable that the translocation of colonic commensal bacteria is closely related to CRC progression. CRC-associated bacteria can serve as a non-invasive and accurate biomarker for CRC diagnosis. In this review, we summarize recent findings on the oncogenic roles of gut bacteria with different anatomical localization in CRC progression.

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The Human Microbiota in Health and Disease
Baohong Wang, Mingfei Yao, Longxian Lv, Zongxin Ling, Lanjuan Li
Engineering    2017, 3 (1): 71-82.
Abstract   HTML   PDF (1171KB)

Trillions of microbes have evolved with and continue to live on and within human beings. A variety of environmental factors can affect intestinal microbial imbalance, which has a close relationship with human health and disease. Here, we focus on the interactions between the human microbiota and the host in order to provide an overview of the microbial role in basic biological processes and in the development and progression of major human diseases such as infectious diseases, liver diseases, gastrointestinal cancers, metabolic diseases, respiratory diseases, mental or psychological diseases, and autoimmune diseases. We also review important advances in techniques associated with microbial research, such as DNA sequencing, metabonomics, and proteomics combined with computation-based bioinformatics. Current research on the human microbiota has become much more sophisticated and more comprehensive. Therefore, we propose that research should focus on the host-microbe interaction and on cause-effect mechanisms, which could pave the way to an understanding of the role of gut microbiota in health and disease. and provide new therapeutic targets and treatment approaches in clinical practice.

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Whether Probiotic Supplementation Benefits Rheumatoid Arthritis Patients: A Systematic Review and Meta-Analysis
Hudan Pan, Runze Li, Ting Li, Jun Wang, Liang Liu
Engineering    2017, 3 (1): 115-121.
Abstract   HTML   PDF (934KB)

Gut and oral microflora are important factors in the pathogenesis and development of rheumatoid arthritis (RA). Recent studies have shown that probiotic supplements have beneficial consequences on experimental arthritis in rats. However, results from randomized clinical trials on the effects of probiotics have not been consistent. The aim of this study was to systematically review the existing evidence for the effects of probiotic intervention in RA. We included randomized controlled trials (RCTs) of RA patients receiving stable treatment with disease-modifying anti-rheumatic drugs (DMARDs) that: ① were combined with additional probiotic supplements or ② were combined with either no additional supplements or only a placebo treatment. Statistical analysis was performed using Review Manager 5.3.3. Six randomized clinical trials were eligible for inclusion in the meta-analysis, with 249 participants in total. The results showed that the probiotic intervention treatment has not yet achieved significant improvement in the American College of Rheumatology 20% improvement criteria (ACR20) score and the disease activity score in 28 joints (DAS28). The laboratory index C-reactive protein (CRP) (mg·L−1) was significantly reduced in the intervention group. The expression of inflammatory cytokines tumor necrosis factor (TNF)-α and interleukine (IL)-1β was also significantly reduced, while IL-10 expression increased in the probiotic intervention groups. This article is the first systematic review and meta-analysis providing a comprehensive assessment of the benefits of treating RA with probiotics. We found that probiotic supplementation may show a limited improvement in RA therapy in existing reports because of a lack of sufficiently high-quality work on the part of clinicians. More multi-centered, large-sample RCTs are needed in order to evaluate the benefits of probiotics in RA treatment.

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Modulation of Gut Microbiota in Pathological States
Yulan Wang, Baohong Wang, Junfang Wu, Xiangyang Jiang, Huiru Tang, Ole H. Nielsen
Engineering    2017, 3 (1): 83-89.
Abstract   HTML   PDF (628KB)

The human microbiota is an aggregate of microorganisms residing in the human body, mostly in the gastrointestinal tract (GIT). Our gut microbiota evolves with us and plays a pivotal role in human health and disease. In recent years, the microbiota has gained increasing attention due to its impact on host metabolism, physiology, and immune system development, but also because the perturbation of the microbiota may result in a number of diseases. The gut microbiota may be linked to malignancies such as gastric cancer and colorectal cancer. It may also be linked to disorders such as nonalcoholic fatty liver disease (NAFLD); obesity and diabetes, which are characterized as “lifestyle diseases” of the industrialized world; coronary heart disease; and neurological disorders. Although the revolution in molecular technologies has provided us with the necessary tools to study the gut microbiota more accurately, we need to elucidate the relationships between the gut microbiota and several human pathologies more precisely, as understanding the impact that the microbiota plays in various diseases is fundamental for the development of novel therapeutic strategies. Therefore, the aim of this review is to provide the reader with an updated overview of the importance of the gut microbiota for human health and the potential to manipulate gut microbial composition for purposes such as the treatment of antibiotic-resistant Clostridium difficile (C. difficile) infections. The concept of altering the gut community by microbial intervention in an effort to improve health is currently in its infancy. However, the therapeutic implications appear to be very great. Thus, the removal of harmful organisms and the enrichment of beneficial microbes may protect our health, and such efforts will pave the way for the development of more rational treatment options in the future.

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