Microbial Ecology along the Gastrointestinal Tract

Regulation of mononuclear phagocyte function by the microbiota at mucosal sites

Mucosal tissues contain distinct microbial communities that differ drastically depending on the barrier site, and as such, mucosal immune responses have evolved to be tailored specifically for their location. Whether protective or regulatory immune responses against invading pathogens or the commensal microbiota occur is controlled by local mononuclear phagocytes (MNPs). Comprising macrophages and dendritic cells (DCs), the functions of these cells are highly dependent on the local environment. For example, the intestine contains the greatest bacterial load of any site in the body, and hence, intestinal MNPs are hyporesponsive to bacterial stimulation. This is thought to be one of the major mechanisms by which harmful immune responses directed against the trillions of harmless bacteria that line the gut lumen are avoided. Regulation of MNP function by the microbiota has been characterized in the most depth in the intestine but there are several mucosal sites that also contain their own microbiota. In this review, we present an overview of how MNP function is regulated by the microbiota at mucosal sites, highlighting recent novel pathways by which this occurs in the intestine, and new studies elucidating these interactions at mucosal sites that have been characterized in less depth, including the urogenital tract.

Sensitivity to Morphine Reward Associates With Gut Dysbiosis in Rats With Morphine-Induced Conditioned Place Preference

Gut microbiota has been found to establish a bidirectional relationship with the central nervous system. Variations of the gut microbiota has been implicated in various mental disorders, including opioid use disorders. Morphine exposure has been repeatedly found to disrupt the gut microbiota, but association between the gut microbiota and the sensitivity to morphine reward remains unknown. In this study the conditioned place preference (CPP) paradigm was used for morphine-treated rats and saline-treated rats. After the CPP procedure, the morphine-treated rats were divided equally into the low and high CPP (L- and H-CPP) groups according to the CPP scores. We adopted 16S rRNA sequencing for the fecal bacterial communities at baseline and post-conditioning. By comparing the morphine-treated group with saline-treated group, we found alterations of microbial composition in the morphine-treated group, but no significant differences in alpha diversity. The L-CPP group and H-CPP group differed in microbial composition both before and after morphine treatment. The relative abundance of certain taxa was correlated to the CPP scores, such as Alloprevotella and Romboutsia. This study provides direct evidence that morphine exposure alters the composition of the gut microbiota in rats and that microbial alterations are correlated to the sensitivity to morphine reward. These findings may help develop novel therapeutic and preventive strategies for opioid use disorder.

Mapping the Segmental Microbiomes in the Human Small Bowel in Comparison with Stool: A REIMAGINE Study

BACKGROUND

Most gut microbiome studies have been performed using stool samples. However, the small intestine is of central importance to digestion, nutrient absorption, and immune function, and characterizing its microbial populations is essential for elucidating their roles in human health and disease.

AIMS

To characterize the microbial populations of different small intestinal segments and contrast these to the stool microbiome.

METHODS

Male and female subjects undergoing esophagogastroduodenoscopy without colon preparation were prospectively recruited. Luminal aspirates were obtained from the duodenum, jejunum, and farthest distance reached. A subset also provided stool samples. 16S rRNA sequencing was performed and analyses were carried out using CLC Genomics Workbench.

RESULTS

16S rRNA sequencing identified differences in more than 2000 operational taxonomic units between the small intestinal and stool microbiomes. Firmicutes and Proteobacteria were the most abundant phyla in the small intestine, and Bacteroidetes were less abundant. In the small intestine, phylum Firmicutes was primarily represented by lactic acid bacteria, including families Streptococcaceae, Lactobacillaceae, and Carnobacteriaceae, and Proteobacteria was represented by families Neisseriaceae, Pasteurellaceae, and Enterobacteriaceae. The duodenal and FD microbial signatures were markedly different from each other, but there were overlaps between duodenal and jejunal and between jejunal and FD microbial signatures. In stool, Firmicutes were represented by families Ruminococcaceae, Lachnospiraceae, Christensenellaceae, and Proteobacteria by class Deltaproteobacteria.

CONCLUSIONS

The small bowel microbiome is markedly different from that in stool and also varies between segments. These findings may be important in determining how compositional changes in small intestinal microbiota contribute to human disease states.

Microbiota changes in a pediatric acute lymphocytic leukemia mouse model

Hematological malignancies are the most common type of pediatric cancers, and acute lymphocytic leukemia (ALL) is the most frequently occurring hematological malignancy during childhood. A major cause of mortality in leukemia is bloodstream infection (BSI). The aim of the current study was to explore the gut microbiota in ALL and its potential functional alterations. High-throughput sequencing was used to characterize the bacterial and fungal microbiota in feces and their predicted functional characteristics in a xenotransplant pediatric ALL mouse model. Our work shows that gut microbiota significantly changes in leukemia, which may result in functional alterations. This study may provide potential therapeutic or preventive strategies of BSI in ALL.

A brief history of periodontics in the United States of America: Pioneers and thought-leaders of the past, and current challenges

This paper summarizes historical events in periodontology in the United States over the past 200 years. The contributions of some of the key thought-leaders of the past are highlighted. Throughout the 20th century, the evolution of thought, leading to the views currently held regarding the pathogenesis and treatment of periodontal diseases, was significantly influenced by: (1) major changes in health-care education; (2) the emergence of periodontics as a specialty of dentistry; (3) the publication of peer-reviewed journals with an emphasis on periodontology; (4) formation of the National Institute of Dental and Craniofacial Research (NIDCR); and (5) expansion of periodontal research programs by the NIDCR. The two major future challenges facing periodontal research are development of a better understanding of the ecological complexities of host-microbial interactions in periodontal health and disease, and identification of the relevant mechanisms involved in the predictable regeneration of damaged periodontal tissues.

An intravital window to image the colon in real time

Intravital microscopy is a powerful technique to observe dynamic processes with single-cell resolution in live animals. No intravital window has been developed for imaging the colon due to its anatomic location and motility, although the colon is a key organ where the majority of microbiota reside and common diseases such as inflammatory bowel disease, functional gastrointestinal disorders, and colon cancer occur. Here we describe an intravital murine colonic window with a stabilizing ferromagnetic scaffold for chronic imaging, minimizing motion artifacts while maximizing long-term survival by preventing colonic obstruction. Using this setup, we image fluorescently-labeled stem cells, bacteria, and immune cells in live animal colons. Furthermore, we image nerve activity via calcium imaging in real time to demonstrate that electrical sacral nerve stimulation can activate colonic enteric neurons. The simple implantable apparatus enables visualization of live processes in the colon, which will open the window to a broad range of studies.

Performing intravital imaging of the colon in mouse models is challenging due to the colon’s anatomic location and motility. Here, the authors develop a murine colonic window for intravital chronic imaging that maximises long-term animal survival and minimises motion artefacts.

Global burden of colorectal cancer: emerging trends, risk factors and prevention strategies

Globally, colorectal cancer (CRC) is the third most commonly diagnosed malignancy and the second leading cause of cancer death. Arising through three major pathways, including adenoma-carcinoma sequence, serrated pathway and inflammatory pathway, CRC represents an aetiologically heterogeneous disease according to subtyping by tumour anatomical location or global molecular alterations. Genetic factors such as germline MLH1 and APC mutations have an aetiologic role, predisposing individuals to CRC. Yet, the majority of CRC is sporadic and largely attributable to the constellation of modifiable environmental risk factors characterizing westernization (for example, obesity, physical inactivity, poor diets, alcohol drinking and smoking). As such, the burden of CRC is shifting towards low-income and middle-income countries as they become westernized. Furthermore, the rising incidence of CRC at younger ages (before age 50 years) is an emerging trend. This Review provides a comprehensive summary of CRC epidemiology, with emphasis on modifiable lifestyle and nutritional factors, chemoprevention and screening. Overall, the optimal reduction of CRC incidence and mortality will require concerted efforts to reduce modifiable risk factors, to leverage chemoprevention research and to promote population-wide and targeted screening.

Comparative analysis of microbiota along the length of the gastrointestinal tract of two tree squirrel species (Sciurus aberti and S. niger) living in sympatry

Microbiota inhabiting the gastrointestinal (GI) tract of animals has important impacts on many host physiological processes. Although host diet is a major factor influencing the composition of the gut micro-organismal community, few comparative studies have considered how differences in diet influence community composition across the length of the GI tract. We used 16S sequencing to compare the microbiota along the length of the GI tract in Abert's (Sciurus aberti) and fox squirrels (S. niger) living in the same habitat. While fox squirrels are generalist omnivores, the diet of Abert's squirrels is unusually high in plant fiber, particularly in winter when they extensively consume fiber-rich inner bark of ponderosa pine (Pinus ponderosa). Consistent with previous studies, microbiota of the upper GI tract of both species consisted primarily of facultative anaerobes and was less diverse than that of the lower GI tract, which included mainly obligate anaerobes. While we found relatively little differentiation between the species in the microbiota of the upper GI tract, the community composition of the lower GI tract was clearly delineated. Notably, the Abert's squirrel lower GI community was more stable in composition and enriched for microbes that play a role in the degradation of plant fiber. In contrast, overall microbial diversity was higher in fox squirrels. We hypothesize that these disparities reflect differences in diet quality and diet breadth between the species.

Gut Microbiota and Obesity: A Role for Probiotics

Nowadays, obesity is one of the most prevalent human health problems. Research from the last 30 years has clarified the role of the imbalance between energy intake and expenditure, unhealthy lifestyle, and genetic variability in the development of obesity. More recently, the composition and metabolic functions of gut microbiota have been proposed as being able to affect obesity development. Here, we will report the current knowledge on the definition, composition, and functions of intestinal microbiota. We have performed an extensive review of the literature, searching for the following keywords: metabolism, gut microbiota, dysbiosis, obesity. There is evidence for the association between gut bacteria and obesity both in infancy and in adults. There are several genetic, metabolic, and inflammatory pathophysiological mechanisms involved in the interplay between gut microbes and obesity. Microbial changes in the human gut can be considered a factor involved in obesity development in humans. The modulation of the bacterial strains in the digestive tract can help to reshape the metabolic profile in the human obese host as suggested by several data from animal and human studies. Thus, a deep revision of the evidence pertaining to the use probiotics, prebiotics, and antibiotics in obese patients is conceivable

The Role of Probiotics in Nonalcoholic Fatty Liver Disease: A New Insight into Therapeutic Strategies

Nonalcoholic fatty liver disease (NAFLD) encompasses a broad spectrum of pathological hepatic conditions ranging from simple steatosis to nonalcoholic steatohepatitis (NASH), which may predispose to liver cirrhosis and hepatocellular carcinoma (HCC). Due to the epidemic obesity, NAFLD is representing a global health issue and the leading cause of liver damage worldwide. The pathogenesis of NAFLD is closely related to insulin resistance (IR), adiposity and physical inactivity as well as genetic and epigenetic factors corroborate to the development and progression of hepatic steatosis and liver injury. Emerging evidence has outlined the implication of gut microbiota and gut-derived endotoxins as actively contributors to NAFLD pathophysiology probably due to the tight anatomo-functional crosstalk between the gut and the liver. Obesity, nutrition and environmental factors might alter intestinal permeability producing a favorable micro-environment for bacterial overgrowth, mucosal inflammation and translocation of both invasive pathogens and harmful byproducts, which, in turn, influence hepatic fat composition and exacerbated pro-inflammatory and fibrotic processes. To date, no therapeutic interventions are available for NAFLD prevention and management, except for modifications in lifestyle, diet and physical exercise even though they show discouraging results due to the poor compliance of patients. The premise of this review is to discuss the role of gut–liver axis in NAFLD and emphasize the beneficial effects of probiotics on gut microbiota composition as a novel attractive therapeutic strategy to introduce in clinical practice.

Optimizing microbiome sequencing for small intestinal aspirates: validation of novel techniques through the REIMAGINE study

Background

The human small intestine plays a central role in the processes of digestion and nutrient absorption. However, characterizations of the human gut microbiome have largely relied on stool samples, and the associated methodologies are ill-suited for the viscosity and low microbial biomass of small intestine samples. As part of the REIMAGINE study to examine the specific roles of the small bowel microbiome in human health and disease, this study aimed to develop and validate methodologies to optimize microbial analysis of the small intestine.

Results

Subjects undergoing esophagogastroduodenoscopy without colon preparation for standard of care were prospectively recruited, and ~ 2 ml samples of luminal fluid were obtained from the duodenum using a custom sterile aspiration catheter. Samples of duodenal aspirates were either untreated (DA-U, N = 127) or pretreated with dithiothreitol (DA-DTT, N = 101), then cultured on MacConkey agar for quantitation of aerobic gram-negative bacteria, typically from the class Gammaproteobacteria, and on blood agar for quantitation of anaerobic microorganisms. DA-DTT exhibited 2.86-fold greater anaerobic bacterial counts compared to DA-U (P = 0.0101), but were not statistically different on MacConkey agar.

DNA isolation from DA-U (N = 112) and DA-DTT (N = 43) samples and library preparation for 16S rRNA gene sequencing were also performed using modified protocols. DA-DTT samples exhibited 3.81-fold higher DNA concentrations (P = 0.0014) and 4.18-fold higher 16S library concentrations (P < 0.0001) then DA-U samples. 16S rRNA gene sequencing revealed increases in the detected relative abundances of obligate and facultative anaerobes in DA-DTT samples, including increases in the genera Clostridium (false discovery rate (FDR) P = 4.38E-6), Enterococcus (FDR P = 2.57E-8), Fusobacterium (FDR P = 0.02) and Bacteroides (FDR P = 5.43E-9). Detected levels of Gram-negative enteropathogens from the phylum Proteobacteria, such as Klebsiella (FDR P = 2.73E-6) and Providencia (FDR P < 0.0001) (family Enterobacteriaceae) and Pseudomonas (family Pseudomonadaceae) (FDR P = 0.04), were also increased in DA-DTT samples.

Conclusions

This study validates novel DTT-based methodology which optimizes microbial culture and 16S rRNA gene sequencing for the study of the small bowel microbiome. The microbial analyses indicate increased isolation of facultative and obligate anaerobes from the mucus layer using these novel techniques.

Plants mentioned in the Islamic Scriptures (Holy Qur'ân and Ahadith): Traditional uses and medicinal importance in contemporary times

ETHNOPHARMACOLOGICAL RELEVANCE

Over the past thousand years, Islamic physicians have collected cultural, philosophical, sociological and historical backgrounds for understanding diseases and medications. The Prophet Mohammed (Peace Be Upon Him (PBUH) said: "There is no disease that Allah has created, except that Allah also has created its cure." Therefore, Islamic scholars are encouraged to explore and use both traditional and modern forms of medicine.

AIM OF THE STUDY

(1) To identify some of the medicinal plants mentioned in the Holy Qur'ân and Ahadith textbooks of the period 700-1500 AD; (2) to compare them with presently used traditional medicines; (3) to evaluate their value based on modern research; and (4) to investigate the contributions of Islamic scholars to the development of the scientific branches, particularly medicine.

MATERIALS AND METHODS

A literature search was performed relating to 12 medicinal plants mentioned in the Holy Qur'ân and Ahadith using textbooks, Al-Azhar scholars, published articles, the plant list website (http://www.theplantlist.org/), the medicinal plant names services website (http://mpns.kew.org/mpns-portal/) and web databases (PubMed, Science Direct, and Google Scholar).

RESULTS AND DISCUSSION

The Islamic Golden Age was a step towards modern medicine, with unique insights and multi-disciplinary aspects. Traditional Islamic Medicine has had a significant impact on the development of various medical, scientific and educational activities. Innumerable Muslim and non-Muslim physicians have built on the strong foundation of Traditional Islamic Medicine by translating the described natural remedies and effects. The influences of different ancient cultures on the traditional uses of natural products were also documented in Islamic Scriptures in the last part of the second millennium. The divine teachings of Islam combine natural and practical healing and incorporate inherited science and technology.

CONCLUSION

In this review, we discuss Traditional Islamic Medicine with reference to both medical recommendations mentioned in the Holy Qur'ân and Prophetic Traditional Medicine (al-Tibb al-Nabawi). Although the molecular mechanisms and functions of some of the listed medicinal plants and their derivatives have been intensively studied, some traditional remedies have yet to be translated into clinical applications.

The Role of Gut-Derived Microbial Antigens on Liver Fibrosis Initiation and Progression

Intestinal dysbiosis has recently become known as an important driver of gastrointestinal and liver disease. It remains poorly understood, however, how gastrointestinal microbes bypass the intestinal mucosa and enter systemic circulation to enact an inflammatory immune response. In the context of chronic liver disease (CLD), insults that drive hepatic inflammation and fibrogenesis (alcohol, fat) can drastically increase intestinal permeability, hence flooding the liver with gut-derived microbiota. Consequently, this may result in exacerbated liver inflammation and fibrosis through activation of liver-resident Kupffer and stellate cells by bacterial, viral, and fungal antigens transported to the liver via the portal vein. This review summarizes the current understanding of microbial translocation in CLD, the cell-specific hepatic response to intestinal antigens, and how this drives the development and progression of hepatic inflammation and fibrosis. Further, we reviewed current and future therapies targeting intestinal permeability and the associated, potentially harmful anti-microbial immune response with respect to their potential in terms of limiting the development and progression of liver fibrosis and end-stage cirrhosis.

Microbial Metabolites Determine Host Health and the Status of Some Diseases

The gastrointestinal (GI) tract is a highly complex organ composed of the intestinal epithelium layer, intestinal microbiota, and local immune system. Intestinal microbiota residing in the GI tract engages in a mutualistic relationship with the host. Different sections of the GI tract contain distinct proportions of the intestinal microbiota, resulting in the presence of unique bacterial products in each GI section. The intestinal microbiota converts ingested nutrients into metabolites that target either the intestinal microbiota population or host cells. Metabolites act as messengers of information between the intestinal microbiota and host cells. The intestinal microbiota composition and resulting metabolites thus impact host development, health, and pathogenesis. Many recent studies have focused on modulation of the gut microbiota and their metabolites to improve host health and prevent or treat diseases. In this review, we focus on the production of microbial metabolites, their biological impact on the intestinal microbiota composition and host cells, and the effect of microbial metabolites that contribute to improvements in inflammatory bowel diseases and metabolic diseases. Understanding the role of microbial metabolites in protection against disease might offer an intriguing approach to regulate disease.

Gut Vibes in Parkinson's Disease: The Microbiota-Gut-Brain Axis

Background

The complexity of the pathogenic mechanisms underlying neurodegenerative disorders such as Parkinson's disease (PD) is attributable to multifactorial changes occurring at a molecular level, influenced by genetics and environmental interactions. However, what causes the main hallmarks of PD is not well understood. Recent data increasingly suggest that imbalances in the gut microbiome composition might trigger and/or exacerbate the progression of PD.

Objective

The present review aims to (1) report emerging literature showing changes in microbiota composition of PD patients compared to healthy individuals and (2) discuss how these changes may initiate and/or perpetuate PD pathology.

Methods

We analyzed 13 studies published from 2015 and included in this review. Altered microbial taxa were compiled in a detailed table summarizing bacterial changes in fecal/mucosal samples. The methodology was systematically reviewed across the articles and was also included in a table to facilitate comparisons between studies.

Results

Multiple studies found a reduction in short-chain fatty-acid-producing bacteria that can rescue neuronal damage through epigenetic mechanisms. Overall, the studies showed that changes in the gut microbiota composition might influence colonic inflammation, gut permeability, and α-synuclein aggregation, contributing to the neurogenerative process.

Conclusion

Further studies with larger cohorts and high-resolution sequencing methods are required to better define gut microbiota changes in PD. Furthermore, additional longitudinal studies are required to determine the causal link between these changes and PD pathogenesis as well as to study the potential of the intestinal microbiota as a biomarker.

Microbiome is a functional modifier of P450 drug metabolism

Host cytochrome P450s (P450s) play important roles in the bioactivation and detoxification of numerous therapeutic drugs, environmental toxicants, dietary factors, as well as endogenous compounds. Gut microbiome is increasingly recognized as our "second genome" that contributes to the xenobiotic biotransformation of the host, and the first pass metabolism of many orally exposed chemicals is a joint effort between host drug metabolizing enzymes including P450s and gut microbiome. Gut microbiome contributes to the drug metabolism via two distinct mechanisms: direct mechanism refers to the metabolism of drugs by microbial enzymes, among which reduction and hydrolysis (or deconjugation) are among the most important reactions; whereas indirect mechanism refers to the influence of host receptors and signaling pathways by microbial metabolites. Many types of microbial metabolites, such as secondary bile acids (BAs), short chain fatty acids (SCFAs), and tryptophan metabolites, are known regulators of human diseases through modulating host xenobiotic-sensing receptors. To study the roles of gut microbiome in regulating host drug metabolism including P450s, several models including germ free mice, antibiotics or probiotics treatments, have been widely used. The present review summarized the current information regarding the interactions between microbiome and the host P450s in xenobiotic biotransformation organs such as liver, intestine, and kidney, highlighting the remote sensing mechanisms underlying gut microbiome mediated regulation of host xenobiotic biotransformation. In addition, the roles of bacterial, fungal, and other microbiome kingdom P450s, which is an understudied area of research in pharmacology and toxicology, are discussed.

Microbial regulation of microRNA expression in the brain-gut axis

The gut microbiome facilitates a consistent transfer of information between the gut and the brain and microRNAs may now represent a key signalling molecule that facilitates this relationship. This review will firstly examine how these small non-coding RNAs influence the gut microbiome, and secondly how the microbiome, when disturbed, may influence miRNA expression in the brain. In addition, we will examine the consequence that microbiome-related changes in miRNA expression have on neurodevelopment, behaviour and cognition. We will also discuss novel data that suggests miRNAs contained in our diet may influence our immune system in a positive manner, offering a further potential pathway for treatment of disorders of the gut-brain axis that are influenced by the microbiome.

Molecular ecology of the yet uncultured bacterial Ct85-cluster in the mammalian gut

In our previous studies on irritable bowel syndrome (IBS) -associated microbiota by molecular methods, we demonstrated that a particular 16S rRNA gene amplicon was more abundant in the feces of healthy subjects or mixed type IBS (IBS-M) -sufferers than in the feces of individuals with diarrhea-type IBS (IBS-D). In the current study, we demonstrated that this, so called Ct85-amplicon, consists of a cluster of very heterogeneous 16S rRNA gene sequences, and defined six 16S rRNA gene types, a to f, within this cluster, each representing a novel species-, genus- or family level taxon. We then designed specific PCR primers for these sequence types, mapped the distribution of the Ct85-cluster sequences and that of the newly defined sequence types in several animal species and compared the sequence types present in the feces of healthy individuals and IBS sufferers using two IBS study cohorts, Finnish and Dutch. Various Ct85-cluster sequence types were detected in the fecal samples of several companion and production animal species with remarkably differing prevalences and abundances. The Ct85 sequence type composition of swine closely resembled that of humans. One of the five types (d) shared between humans and swine was not present in any other animals tested, while one sequence type (b) was found only in human samples. In both IBS study cohorts, one type (e) was more prevalent in healthy individuals than in the IBS-M group. By revealing various sequence types in the widespread Ct85-cluster and their distribution, the results improve our understanding of these uncultured bacteria, which is essential for future efforts to cultivate representatives of the Ct85-cluster and reveal their roles in IBS.

Helminth-microbiota cross-talk - A journey through the vertebrate digestive system

The gastrointestinal (GI) tract of vertebrates is inhabited by a vast array of organisms, i.e., the microbiota and macrobiota. The former is composed largely of commensal microorganisms, which play vital roles in host nutrition and maintenance of energy balance, in addition to supporting the development and function of the vertebrate immune system. By contrast, the macrobiota includes parasitic helminths, which are mostly considered detrimental to host health via a range of pathogenic effects that depend on parasite size, location in the GI tract, burden of infection, metabolic activity, and interactions with the host immune system. Sharing the same environment within the vertebrate host, the GI microbiota and parasitic helminths interact with each other, and the results of such interactions may impact, directly or indirectly, on host health and homeostasis. The complex relationships occurring between parasitic helminths and microbiota have long been neglected; however, recent studies point towards a role for these interactions in the overall pathophysiology of helminth disease, as well as in parasite-mediated suppression of inflammation. Whilst several discrepancies in qualitative and quantitative modifications in gut microbiota composition have been described based on host and helminth species under investigation, we argue that attention should be paid to the systems biology of the gut compartment under consideration, as variations in the abundances of the same population of bacteria inhabiting different niches of the GI tract may result in varying functional consequences for host physiology.

Early-Life Iron Deficiency and Subsequent Repletion Alters Development of the Colonic Microbiota in the Pig

Background: Iron deficiency is the most prevalent micronutrient deficiency worldwide, affecting over two billion people. Early-life iron deficiency may alter the developing microbiota, which may or may not be reversible with subsequent dietary iron repletion. Thus, the aim of this study was to determine whether early-life iron deficiency and subsequent repletion alter colonic microbial composition and fermentation end-product concentrations in pigs. Methods: Forty-two male pigs received either control (CONT, 21.3 mg Fe/L) or iron-deficient (ID, 2.72 mg Fe/L) milk replacer treatments from postnatal day (PND) 2 to 32. Subsequently, 20 pigs continued through a series of age-appropriate, iron-adequate diets from PND 33 to 61. Contents from the ascending colon (AC) and rectum (feces) were collected at PND 32 and/or 61. Assessments included microbiota composition by 16S rRNA sequencing and volatile fatty acid (VFA) concentrations by gas chromatography methods. Data were analyzed using a 1-way ANOVA and PERMANOVA to assess the main effects of early-life iron status on all outcomes. Results: In AC samples, 15 genera differed (P < 0.05) between ID and CONT pigs, while 27 genera differed (P < 0.05) in fecal samples at PND 32. Early-life ID pigs had higher (P = 0.012) relative abundance of Lactobacillus in AC samples compared with CONT pigs. In feces, ID pigs had lower (P < 0.05) relative abundances of Bacteroides and Clostridium from the families of Clostridiaceae, Lachnospiraceae, and Ruminococcaceae. At PND 61, only two genera differed between treatment groups in AC samples, with ID pigs having a higher (P = 0.043) relative abundance of Bifidobacterium and lower (P = 0.047) relative abundance of Prevotella. Beta diversity differed at PND 32 in both AC and feces between CONT and ID pigs but no differences remained at PND 61. At PND 32, the total VFA concentration was higher in ID pigs compared with CONT pigs in both AC (P = 0.003) and feces (P = 0.001), but no differences in VFA concentrations persisted to PND 61. Conclusion: Early-life iron status influenced microbial composition and VFA concentrations within the large intestine, but these differences were largely normalized following subsequent dietary iron repletion.

Fusobacterium nucleatum, the communication with colorectal cancer

Colorectal cancer (CRC) is the fourth most common cancer in 2018 with poor prognosis. Fusobacterium nucleatum (F.n), an anaerobe, is found to be enriched in both stools and tumor tissues of CRC patients. As surveys show, tumor initiates before the collection of F.n. In return, F.n helps cancer cells to build up tumor microenvironment and benefit for their chemo-resistant. The elements constituted the tumor environment, including neutrophils, macrophages and lymphocytes, contribute to the existing of tumor cells respectively. However, the integrated and interactive roles of those elements are poorly investigated. The intracellular molecular alteration MSI is a result of F.n infection and the microbiology-molecular pathological epidemiology (MPE) has become a new trend to analysis F.n and tumorigenesis. Chemoresistance of tumor cells is also affected by F.n induced microenvironment, or F.n achieves it directly. Finally, F.n could be a biomarker of CRC. All in all, our review will lay a foundation for the therapy of CRC through the interference of F.n and perspective to follow-up studies.

Scales of persistence: transmission and the microbiome

Historically microbiomes have been studied on the scale of the individual host, giving little consideration for the role of extra-host microbial populations in microbiome assembly. However, work in recent years has brought to light the importance of inter-host transmission and its influence on microbiome composition and dynamics. We now appreciate that microbiomes do not exist in isolation, but exchange constituents with the microbial communities of other hosts and the environment. Moving forward, fully understanding the role of transmission in microbiome assembly and dynamics will require a high-resolution view of the colonization and persistence patterns of particular microbial lineages (i.e. strains) across individuals and the environment. Yet, accomplishing this level of resolution will be an immense challenge, requiring improved sampling and bioinformatics approaches as well as employment of tractable experimental models. Insight gained from these investigations will contribute to our understanding of microbiome composition and variation, and lead to improved strategies for modulating microbiomes to improve human health.

Gut Microbiome: Profound Implications for Diet and Disease

The gut microbiome plays an important role in human health and influences the development of chronic diseases ranging from metabolic disease to gastrointestinal disorders and colorectal cancer. Of increasing prevalence in Western societies, these conditions carry a high burden of care. Dietary patterns and environmental factors have a profound effect on shaping gut microbiota in real time. Diverse populations of intestinal bacteria mediate their beneficial effects through the fermentation of dietary fiber to produce short-chain fatty acids, endogenous signals with important roles in lipid homeostasis and reducing inflammation. Recent progress shows that an individual’s starting microbial profile is a key determinant in predicting their response to intervention with live probiotics. The gut microbiota is complex and challenging to characterize. Enterotypes have been proposed using metrics such as alpha species diversity, the ratio of Firmicutes to Bacteroidetes phyla, and the relative abundance of beneficial genera (e.g., Bifidobacterium, Akkermansia) versus facultative anaerobes (E. coli), pro-inflammatory Ruminococcus, or nonbacterial microbes. Microbiota composition and relative populations of bacterial species are linked to physiologic health along different axes. We review the role of diet quality, carbohydrate intake, fermentable FODMAPs, and prebiotic fiber in maintaining healthy gut flora. The implications are discussed for various conditions including obesity, diabetes, irritable bowel syndrome, inflammatory bowel disease, depression, and cardiovascular disease.

The Microbiota and the Immune Response: What Is the Chicken and What Is the Egg?

The underlying factors driving the onset and progression of inflammatory bowel disease (IBD) include the interplay between host genetics, microbiota, and mucosal inflammation. The same environmental triggers that are a risk factor for IBD also alter the microbiota, suggesting a link between the microbiome and IBD. Specific IBD-associated genetic polymorphisms change the microbiome linking host genetics to the microbiota. Microbial changes occur at least simultaneously with new onset IBD, and fecal microbial transplant can ameliorate certain types of IBD. A current debate in the field is which comes first, dysbiosis or inflammation? Can restitution of the microbiome "cure" IBD?

Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health

The human gut microbiome is a critical component of digestion, breaking down complex carbohydrates, proteins, and to a lesser extent fats that reach the lower gastrointestinal tract. This process results in a multitude of microbial metabolites that can act both locally and systemically (after being absorbed into the bloodstream). The impact of these biochemicals on human health is complex, as both potentially beneficial and potentially toxic metabolites can be yielded from such microbial pathways, and in some cases, these effects are dependent upon the metabolite concentration or organ locality. The aim of this review is to summarize our current knowledge of how macronutrient metabolism by the gut microbiome influences human health. Metabolites to be discussed include short-chain fatty acids and alcohols (mainly yielded from monosaccharides); ammonia, branched-chain fatty acids, amines, sulfur compounds, phenols, and indoles (derived from amino acids); glycerol and choline derivatives (obtained from the breakdown of lipids); and tertiary cycling of carbon dioxide and hydrogen. Key microbial taxa and related disease states will be referred to in each case, and knowledge gaps that could contribute to our understanding of overall human wellness will be identified.

Bringing microbiome-drug interaction research into the clinic

Our understanding of the scope and clinical relevance of gut microbiota metabolism of drugs is limited to relatively few biotransformations targeting a subset of therapeutics. Translating microbiome research into the clinic requires, in part, a mechanistic and predictive understanding of microbiome-drug interactions. This review provides an overview of microbiota chemistry that shapes drug efficacy and toxicity. We discuss experimental and computational approaches that attempt to bridge the gap between basic and clinical microbiome research. We highlight the current landscape of preclinical research focused on identifying microbiome-based biomarkers of patient drug response and we describe clinical trials investigating approaches to modulate the microbiome with the goal of improving drug efficacy and safety. We discuss approaches to aggregate clinical and experimental microbiome features into predictive models and review open questions and future directions toward utilizing the gut microbiome to improve drug safety and efficacy.

Vitamin A and vitamin D regulate the microbial complexity, barrier function, and the mucosal immune responses to ensure intestinal homeostasis

Diet is an important regulator of the gastrointestinal microbiota. Vitamin A and vitamin D deficiencies result in less diverse, dysbiotic microbial communities and increased susceptibility to infection or injury of the gastrointestinal tract. The vitamin A and vitamin D receptors are nuclear receptors expressed by the host, but not the microbiota. Vitamin A- and vitamin D-mediated regulation of the intestinal epithelium and mucosal immune cells underlies the effects of these nutrients on the microbiota. Vitamin A and vitamin D regulate the expression of tight junction proteins on intestinal epithelial cells that are critical for barrier function in the gut. Other shared functions of vitamin A and vitamin D include the support of innate lymphoid cells that produce IL-22, suppression of IFN-γ and IL-17 by T cells, and induction of regulatory T cells in the mucosal tissues. There are some unique functions of vitamin A and D; for example, vitamin A induces gut homing receptors on T cells, while vitamin D suppresses gut homing receptors on T cells. Together, vitamin A- and vitamin D-mediated regulation of the intestinal epithelium and mucosal immune system shape the microbial communities in the gut to maintain homeostasis.

High-Esterified Pectin Reverses Metabolic Malprogramming, Improving Sensitivity to Adipostatic/Adipokine Hormones

Detrimental metabolic programming has become a determinant factor in obesity propensity and the development of metabolic disorders; therefore, the search of nutritional strategies to reverse it is very relevant. Pectin is a prebiotic with health-promoting effects, such as control of glucose homeostasis and lipid metabolism, although other possible health effects and the prevention of obesity have been poorly studied. We studied the effects of chronic physiological supplementation with high-esterified pectin (HEP) in the reversion of metabolic nutrition-sensitive malprogramming associated with gestational undernutrition. As a model of nutrition-sensitive malprogramming, we used the progeny of rats with mild calorie restriction (CR) during pregnancy and analyzed their performance under metabolic stress (high-sucrose diet). We focused on the study of the sensitivity to the main adipostatic/adipokine hormones, i.e., leptin, insulin, and adiponectin, at both peripheral (liver and circulating parameters) and central (hypothalamus) levels. Our main findings suggest that chronic HEP supplementation is able to prevent weight/fat gain, to substantially reverse the detrimental malprogramming caused by the CR condition, to improve general health circulating markers, to modulate oxidative/lipogenic balance in the liver and energy metabolism regulators in the hypothalamus, and to restore/improve adipostatic/adipokine sensitivity affected by maternal calorie restriction, both peripherally and centrally. HEP stands out as a food component potentially useful against the development of metabolic disorders and obesity.

Serotonin Transporter Deficiency is Associated with Dysbiosis and Changes in Metabolic Function of the Mouse Intestinal Microbiome

Serotonin transporter (SERT) plays a critical role in regulating extracellular availability of serotonin (5-HT) in the gut and brain. Mice with deletion of SERT develop metabolic syndrome as they age. Changes in the gut microbiota are being increasingly implicated in Metabolic Syndrome and Diabetes. To investigate the relationship between the gut microbiome and SERT, this study assessed the fecal and cecal microbiome profile of 11 to 12 week-old SERT+/+ and SERT-/- mice. Microbial DNA was isolated, processed for metagenomics shotgun sequencing, and taxonomic and functional profiles were assessed. 34 differentially abundant bacterial species were identified between SERT+/+ and SERT-/-. SERT-/- mice displayed higher abundances of Bacilli species including genera Lactobacillus, Streptococcus, Enterococcus, and Listeria. Furthermore, SERT-/- mice exhibited significantly lower abundances of Bifidobacterium species and Akkermansia muciniphilia. Bacterial community structure was altered in SERT-/- mice. Differential abundance of bacteria was correlated with changes in host gene expression. Bifidobacterium and Bacilli species exhibited significant associations with host genes involved in lipid metabolism pathways. Our results show that SERT deletion is associated with dysbiosis similar to that observed in obesity. This study contributes to the understanding as to how changes in gut microbiota are associated with metabolic phenotype seen in SERT deficiency.

Virome biogeography in the lower gastrointestinal tract of rhesus macaques with chronic diarrhea

The composition of gastrointestinal tract viromes has been associated with multiple diseases. Our understanding of virus communities in the GI tract is still very limited due to challenges in sampling from different GI sites. Here we defined the GI viromes of 15 rhesus macaques with chronic diarrhea. Luminal content samples from terminal ileum, proximal and distal colon were collected at necropsy while samples from the rectum were collected antemortem using a fecal loop. The composition of and ecological parameters associated with the terminal ileum virome were distinct from the colon and rectum samples; these differences were driven by bacteriophages rather than eukaryotic viruses. The six contigs that were most discriminative of the viromes were distantly related to bacteriophages from three different families. Our analysis provides support for using fecal loop sampling of the rectum as a proxy of the colonic virome in humans.

Small Intestinal Bacterial Overgrowth in Children: A State-Of-The-Art Review

Small intestinal bacterial overgrowth (SIBO) is a heterogenous and poorly understood entity characterised by an excessive growth of select microorganisms within the small intestine. This excessive bacterial biomass, in turn, disrupts host physiology in a myriad of ways, leading to gastrointestinal and non-gastrointestinal symptoms and complications. SIBO is a common cause of non-specific gastrointestinal symptoms in children, such as chronic abdominal pain, abdominal distention, diarrhoea, and flatulence, amongst others. In addition, it has recently been implicated in the pathophysiology of stunting, a disease that affects millions of children worldwide. Risk factors such as acid-suppressive therapies, alterations in gastrointestinal motility and anatomy, as well as impoverished conditions, have been shown to predispose children to SIBO. SIBO can be diagnosed via culture-dependant or culture-independent approaches. SIBO's epidemiology is limited due to the lack of uniformity and consensus of its diagnostic criteria, as well as the paucity of literature available. Antibiotics remain the first-line treatment option for SIBO, although emerging modalities such as probiotics and diet manipulation could also have a role. Herein, we present a state-of-the-art-review which aims to comprehensively outline the most current information on SIBO in children, with particular emphasis on the gut microbiota.

Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians

Advances in technical capabilities for reading complex human microbiomes are leading to an explosion of microbiome research, leading in turn to intense interest among clinicians in applying these techniques to their patients. In this review, we discuss the content of the human microbiome, including intersubject and intrasubject variability, considerations of study design including important confounding factors, and different methods in the laboratory and on the computer to read the microbiome and its resulting gene products and metabolites. We highlight several common pitfalls for clinicians, including the expectation that an individual's microbiome will be stable, that diet can induce rapid changes that are large compared with the differences among subjects, that everyone has essentially the same core stool microbiome, and that different laboratory and computational methods will yield essentially the same results. We also highlight the current limitations and future promise of these techniques, with the expectation that an understanding of these considerations will help accelerate the path toward routine clinical application of these techniques developed in research settings.

Implications of Probiotics on the Maternal-Neonatal Interface: Gut Microbiota, Immunomodulation, and Autoimmunity

Probiotics are being investigated for the treatment of autoimmune disease by re-balancing dysbiosis induced changes in the immune system. Pregnancy is a health concern surrounding autoimmune disease, both for the mother and her child. Probiotics for maternity are emerging on the market and have gained significant momentum in the literature. Thus far, evidence supports that probiotics alter the structure of the normal microbiota and the microbiota changes significantly during pregnancy. The interaction between probiotics-induced changes and normal changes during pregnancy is poorly understood. Furthermore, there is emerging evidence that the maternal gut microbiota influences the microbiota of offspring, leading to questions on how maternal probiotics may influence the health of neonates. Underpinning the development and balance of the immune system, the microbiota, especially that of the gut, is significantly important, and dysbiosis is an agent of immune dysregulation and autoimmunity. However, few studies exist on the implications of maternal probiotics for the outcome of pregnancy in autoimmune disease. Is it helpful or harmful for mother with autoimmune disease to take probiotics, and would this be protective or pathogenic for her child? Controversy surrounds whether probiotics administered maternally or during infancy are healthful for allergic disease, and their use for autoimmunity is relatively unexplored. This review aims to discuss the use of maternal probiotics in health and autoimmune disease and to investigate their immunomodulatory properties.

Rationale of Probiotic Supplementation during Pregnancy and Neonatal Period

Probiotics are living microorganisms that confer a health benefit when administered in adequate amounts. It has been speculated that probiotics supplementation during pregnancy and in the neonatal period might reduce some maternal and neonatal adverse outcomes. In this narrative review, we describe the rationale behind probiotic supplementation and its possible role in preventing preterm delivery, perinatal infections, functional gastrointestinal diseases, and atopic disorders during early life.

Stunted childhood growth is associated with decompartmentalization of the gastrointestinal tract and overgrowth of oropharyngeal taxa

Linear growth delay (stunting) affects roughly 155 million children under the age of 5 years worldwide. Treatment has been limited by a lack of understanding of the underlying pathophysiological mechanisms. Stunting is most likely associated with changes in the microbial community of the small intestine, a compartment vital for digestion and nutrient absorption. Efforts to better understand the pathophysiology have been hampered by difficulty of access to small intestinal fluids. Here, we describe the microbial community found in the upper gastrointestinal tract of stunted children aged 2-5 y living in sub-Saharan Africa. We studied 46 duodenal and 57 gastric samples from stunted children, as well as 404 fecal samples from stunted and nonstunted children living in Bangui, Central African Republic, and in Antananarivo, Madagascar, using 16S Illumina Amplicon sequencing and semiquantitative culture methods. The vast majority of the stunted children showed small intestinal bacterial overgrowth dominated by bacteria that normally reside in the oropharyngeal cavity. There was an overrepresentation of oral bacteria in fecal samples of stunted children, opening the way for developing noninvasive diagnostic markers. In addition, Escherichia coli/Shigella sp. and Campylobacter sp. were found to be more prevalent in stunted children, while Clostridia, well-known butyrate producers, were reduced. Our data suggest that stunting is associated with a microbiome "decompartmentalization" of the gastrointestinal tract characterized by an increased presence of oropharyngeal bacteria from the stomach to the colon, hence challenging the current view of stunting arising solely as a consequence of small intestine overstimulation through recurrent infections by enteric pathogens.

Identifying the etiology and pathophysiology underlying stunting and environmental enteropathy: study protocol of the AFRIBIOTA project

BACKGROUND

Globally one out of four children under 5 years is affected by linear growth delay (stunting). This syndrome has severe long-term sequelae including increased risk of illness and mortality and delayed psychomotor development. Stunting is a syndrome that is linked to poor nutrition and repeated infections. To date, the treatment of stunted children is challenging as the underlying etiology and pathophysiological mechanisms remain elusive. We hypothesize that pediatric environmental enteropathy (PEE), a chronic inflammation of the small intestine, plays a major role in the pathophysiology of stunting, failure of nutritional interventions and diminished response to oral vaccines, potentially via changes in the composition of the pro- and eukaryotic intestinal communities. The main objective of AFRIBIOTA is to describe the intestinal dysbiosis observed in the context of stunting and to link it to PEE. Secondary objectives include the identification of the broader socio-economic environment and biological and environmental risk factors for stunting and PEE as well as the testing of a set of easy-to-use candidate biomarkers for PEE. We also assess host outcomes including mucosal and systemic immunity and psychomotor development. This article describes the rationale and study protocol of the AFRIBIOTA project.

METHODS

AFRIBIOTA is a case-control study for stunting recruiting children in Bangui, Central African Republic and in Antananarivo, Madagascar. In each country, 460 children aged 2-5 years with no overt signs of gastrointestinal disease are recruited (260 with no growth delay, 100 moderately stunted and 100 severely stunted). We compare the intestinal microbiota composition (gastric and small intestinal aspirates; feces), the mucosal and systemic immune status and the psychomotor development of children with stunting and/or PEE compared to non-stunted controls. We also perform anthropological and epidemiological investigations of the children's broader living conditions and assess risk factors using a standardized questionnaire.

DISCUSSION

To date, the pathophysiology and risk factors of stunting and PEE have been insufficiently investigated. AFRIBIOTA will add new insights into the pathophysiology underlying stunting and PEE and in doing so will enable implementation of new biomarkers and design of evidence-based treatment strategies for these two syndromes.

The role of the gut microbiota on animal model reproducibility

The gut microbiota is composed of approximately 1010-1014 cells, including fungi, bacteria, archaea, protozoa, viruses, and bacteriophages; their genes and their various metabolites were found throughout the gastrointestinal tract. It has co-evolved with each species to assist with day to day bodily functions, such as digestion, metabolism of xenobiotics, development of mucosal immunity and immunomodulation, and protection against invading pathogens. Because of the significant beneficial impact that gut microbiota may have, there is interest in learning more about it and translating these findings into clinical therapies. Results from recent studies characterizing the gut microbiota of various species have demonstrated the range of influences that may affect gut microbiota diversity, including animal strain, obesity, types of enrichment used, bedding and housing methods, treatment with antimicrobials, vendor source, specific animal housing, diet, and intercurrent disease. Relatively little is known about the functional consequences of alterations of the gut microbiota and exactly how changes in richness and diversity of the microbiota translate into changes in health and susceptibility to disease. Furthermore, questions have been raised as to whether germ-free or even ultraclean, barrier-raised mice are relevant models of human disease, given their significantly reduced gut microbiota diversity and complexity compared with conventionally housed mice. In addition, evidence suggests that the specific anatomical location selected for assessing the gut microbiota has a highly significant effect on study outcomes, in that bacterial phyla change significantly along the gastrointestinal tract. This paper will explore animal model reproducibility in light of this information about the gut microbiota.