2016年动物胃肠道微生物组研究十大亮点成果

动物胃肠道微生物对生产性能提高具有重要的作用,因此营养、微生物组与生产表型的互作研究已经成为国际研究热点。综述了2016年动物胃肠道微生物组学研究取得的十项重要成果,这些成果通过组学方法,研究了瘤胃纤维分解菌和尿素分解菌的功能基因多样性,揭示了微生物群落与日粮营养素、宿主基因型、环境的互作关系,阐明了反刍动物生产表型相关的瘤胃微生物种类和功能;首次构建猪肠道微生物组参考基因集,解析猪全肠道黏膜微生物组成,阐明了猪增重相关肠道微生物种类。这十大亮点成果将为国内动物营养学家开展动物胃肠道微生物组学研究提供参考。     

鸡肠道微生物菌群的建立发育、分布和生理学意义

鸡的胃肠道具有复杂的微生物菌群,该微生物菌群与宿主的肠道和整体健康密切相关,为了全面揭示鸡肠道微生物菌群的组成及其功能,本文对鸡肠道微生物菌群的建立发育、各肠段群落的分布及其生理学意义进行综述,从而为鸡肠道功能菌株的分离及有效利用,合理调控微生物菌群-宿主相互作用,提高饲料转化率和改善肠道健康提供理论依据。     

Potential rates of fermentation in digesta from the gastrointestinal tract of pigs: effect of feeding fermented liquid feed

Microbial catabolic capacity in digesta from the gastrointestinal tract of pigs fed either dry feed or fermented liquid feed (FLF) was determined with the PhenePlate multisubstrate system. The in vitro technique was modified to analyze the kinetics of substrate catabolism mediated by the standing stock of enzymes (potential rates of fermentation), allowing a quantitative evaluation of the dietary effect on the catabolic capacity of the microbiota. In total, the potential rates of fermentation were significantly reduced in digesta from the large intestine (cecum, P < 0.1; colon, P < 0.01; and rectum, P < 0.0001) of pigs fed FLF compared to pigs fed dry feed. No effect of diet was observed in the stomach (P = 0.71) or the distal part of the small intestine (P = 0.97). The highest rates of fermentation and the most significant effect of diet were observed for readily fermentable carbohydrates like maltose, sucrose, and lactose. Feeding FLF to pigs also led to a reduction in the large intestine of the total counts of anaerobic bacteria in general and lactic acid bacteria specifically, as well as of microbial activity, as determined by the concentration of ATP and short-chain fatty acids. The low-molecular-weight carbohydrates were fermented mainly to lactic acid in the FLF before being fed to the animals. This may have limited microbial nutrient availability in the digesta reaching the large intestine of pigs fed FLF and may have caused the observed reduction in activity and density of the cecal and colonic microbial population. On the other hand, feeding FLF to pigs reduced the viable counts of coliform bacteria (indicator of Escherichia coli and Salmonella spp.) most profoundly in the stomach and the distal part of the small intestine, probably due to the bactericidal effect of lactic acid and low pH. The results presented clearly demonstrate that feeding FLF to pigs had a great impact on the indigenous microbiota, as reflected in bacterial numbers, short-chain fatty acid concentration, and substrate utilization. However, completely different mechanisms may be involved in the proximal and the distal parts of the gastrointestinal tract. The present study illustrates the utility of the PhenePlate system for quantifying the catabolic capacity of the indigenous gastrointestinal tract microbiota.     

The potential for probiotic manipulation of the gastrointestinal microbiome

Multiple internal and external sites of the healthy human body are colonized by a diversity of symbiotic microbes. The microbial assemblages found in the intestine represent some of the most dense and diverse of these human-associated ecosystems. Unsurprisingly, the enteric microbiome, that is the totality of microbes, their combined genomes, and their interactions with the human body, has a profound impact on physiological aspects of mammalian function, not least, host immune response. Lack of early-life exposure to certain microbes, or shifts in the composition of the gastrointestinal microbiome have been linked to the development and progression of several intestinal and extra-intestinal diseases, including childhood asthma development and inflammatory bowel disease. Modulating microbial exposure through probiotic supplementation represents a long-held strategy towards ameliorating disease via intestinal microbial community restructuring. This field has experienced somewhat of a resurgence over the past few years, primarily due to the exponential increase in human microbiome studies and a growing appreciation of our dependence on resident microbiota to modulate human health. This review aims to review recent regulatory aspects related to probiotics in food. It also summarizes what is known to date with respect to human gastrointestinal microbiota - the niche which has been most extensively studied in the human system - and the evidence for probiotic supplementation as a viable therapeutic strategy for modulating this consortium.     

Potential Rates of Fermentation in Digesta from the Gastrointestinal Tract of Pigs: Effect of Feeding Fermented Liquid Feed

Microbial catabolic capacity in digesta from the gastrointestinal tract of pigs fed either dry feed or fermented liquid feed (FLF) was determined with the PhenePlate multisubstrate system. The in vitro technique was modified to analyze the kinetics of substrate catabolism mediated by the standing stock of enzymes (potential rates of fermentation), allowing a quantitative evaluation of the dietary effect on the catabolic capacity of the microbiota. In total, the potential rates of fermentation were significantly reduced in digesta from the large intestine (cecum, P < 0.1; colon, P < 0.01; and rectum, P < 0.0001) of pigs fed FLF compared to pigs fed dry feed. No effect of diet was observed in the stomach (P = 0.71) or the distal part of the small intestine (P = 0.97). The highest rates of fermentation and the most significant effect of diet were observed for readily fermentable carbohydrates like maltose, sucrose, and lactose. Feeding FLF to pigs also led to a reduction in the large intestine of the total counts of anaerobic bacteria in general and lactic acid bacteria specifically, as well as of microbial activity, as determined by the concentration of ATP and short-chain fatty acids. The low-molecular-weight carbohydrates were fermented mainly to lactic acid in the FLF before being fed to the animals. This may have limited microbial nutrient availability in the digesta reaching the large intestine of pigs fed FLF and may have caused the observed reduction in activity and density of the cecal and colonic microbial population. On the other hand, feeding FLF to pigs reduced the viable counts of coliform bacteria (indicator of Escherichia coli and Salmonella spp.) most profoundly in the stomach and the distal part of the small intestine, probably due to the bactericidal effect of lactic acid and low pH. The results presented clearly demonstrate that feeding FLF to pigs had a great impact on the indigenous microbiota, as reflected in bacterial numbers, short-chain fatty acid concentration, and substrate utilization. However, completely different mechanisms may be involved in the proximal and the distal parts of the gastrointestinal tract. The present study illustrates the utility of the PhenePlate system for quantifying the catabolic capacity of the indigenous gastrointestinal tract microbiota.     

Resorption und Einbau radioaktiv markierter Aminosäuren bei Verabreichung unterschiedlicher Proteinträger an Ratten

Since the announcement of the ban on the use of antibiotics as antimicrobial growth promoters in the feed of pigs in 2006 the investigation towards alternative feed additives has augmented considerably. Although fermented liquid feed is not an additive, but a feeding strategy, the experimental work examining its possible advantages also saw a rise. The use of fermented liquid feed (FLF) has two main advantages, namely that the simultaneous provision of feed and water may result in an alleviation of the transition from the sow milk to solid feed and may also reduce the time spent to find both sources of nutrients, and secondly, that offering FLF with a low pH may strengthen the potential of the stomach as a first line of defence against possible pathogenic infections. Because of these two advantages, FLF is often stated as an ideal feed for weaned piglets. The results obtained so far are rather variable, but in general they show a better body weight gain and worse feed/gain ratio for the piglets. However, for growing-finishing pigs on average a better feed/gain ratio is found compared to pigs fed dry feed. This better performance is mostly associated with less harmful microbiota and better gut morphology. This review provides an overview of the current knowledge of FLF for pigs, dealing with the FLF itself as well as its effect on the gastrointestinal tract and animal performance.     

Fermented liquid feed for pigs

Since the announcement of the ban on the use of antibiotics as antimicrobial growth promoters in the feed of pigs in 2006 the investigation towards alternative feed additives has augmented considerably. Although fermented liquid feed is not an additive, but a feeding strategy, the experimental work examining its possible advantages also saw a rise. The use of fermented liquid feed (FLF) has two main advantages, namely that the simultaneous provision of feed and water may result in an alleviation of the transition from the sow milk to solid feed and may also reduce the time spent to find both sources of nutrients, and secondly, that offering FLF with a low pH may strengthen the potential of the stomach as a first line of defence against possible pathogenic infections. Because of these two advantages, FLF is often stated as an ideal feed for weaned piglets. The results obtained so far are rather variable, but in general they show a better body weight gain and worse feed/gain ratio for the piglets. However, for growing-finishing pigs on average a better feed/gain ratio is found compared to pigs fed dry feed. This better performance is mostly associated with less harmful microbiota and better gut morphology. This review provides an overview of the current knowledge of FLF for pigs,dealing with the FLF itself as well as its effect on the gastrointestinal tract and animal performance.     

Survival and therapeutic potential of probiotic organisms with reference to Lactobacillus acidophilus and Bifidobacterium spp

The present paper provides an overview on the use of probiotic organisms as live supplements, with particular emphasis on Lactobacillus acidophilus and Bifidobacterium spp. The therapeutic potential of these bacteria in fermented dairy products is dependent on their survival during manufacture and storage. Probiotic bacteria are increasingly used in food and pharmaceutical applications to balance disturbed intestinal microflora and related dysfunction of the human gastrointestinal tract. Lactobacillus acidophilus and Bifidobacterium spp. have been reported to be beneficial probiotic organisms that provide excellent therapeutic benefits. The biological activity of probiotic bacteria is due in part to their ability to attach to enterocytes. This inhibits the binding of enteric pathogens by a process of competitive exclusion. Attachment of probiotic bacteria to cell surface receptors of enterocytes also initiates signalling events that result in the synthesis of cytokines. Probiotic bacteria also exert an influence on commensal micro-organisms by the production of lactic acid and bacteriocins. These substances inhibit growth of pathogens and also alter the ecological balance of enteric commensals. Production of butyric acid by some probiotic bacteria affects the turnover of enterocytes and neutralizes the activity of dietary carcinogens, such as nitrosamines, that are generated by the metabolic activity of commensal bacteria in subjects consuming a high-protein diet. Therefore, inclusion of probiotic bacteria in fermented dairy products enhances their value as better therapeutic functional foods. However, insufficient viability and survival of these bacteria remain a problem in commercial food products. By selecting better functional probiotic strains and adopting improved methods to enhance survival, including the use of appropriate prebiotics and the optimal combination of probiotics and prebiotics (synbiotics), an increased delivery of viable bacteria in fermented products to the consumers can be achieved.     

Review: The development of the gastrointestinal tract microbiota and intervention in neonatal ruminants

The complex microbiome colonizing the gastrointestinal tract (GIT) of ruminants plays an important role in the development of the immune system, nutrient absorption and metabolism. Hence, understanding GIT microbiota colonization in neonatal ruminants has positive impacts on host health and productivity. Microbes rapidly colonize the GIT after birth and gradually develop into a complex microbial community, which allows the possibility of GIT microbiome manipulation to enhance newborn health and growth and perhaps induce lasting effects in adult ruminants. This paper reviews recent advances in understanding how host-microbiome interactions affect the GIT development and health of neonatal ruminants. Following initial GIT microbiome colonization, continuous exposure to host-specific microorganisms is necessary for GIT development and immune system maturation. Furthermore, the early GIT microbial community structure is significantly affected by early life events, such as maternal microbiota exposure, dietary changes, age and the addition of prebiotics, probiotics and synbiotics, supporting the idea of microbial programming in early life. However, the time window in which interventions can optimally improve production and reduce gastrointestinal disease as well as the role of key host-specific microbiota constituents and host immune regulation requires further study.     

Microbial Metabolites and Intestinal Stem Cells Tune Intestinal Homeostasis

Microorganisms that colonize the gastrointestinal tract, collectively known as the gut microbiota, are known to produce small molecules and metabolites that significantly contribute to host intestinal development, functions, and homeostasis. Emerging insights from microbiome research reveal that gut microbiota‐derived signals and molecules influence another key player maintaining intestinal homeostasis—the intestinal stem cell niche, which regulates epithelial self‐renewal. In this review, the literature on gut microbiota‐host crosstalk is surveyed, highlighting the effects of gut microbial metabolites on intestinal stem cells. The production of various classes of metabolites, their actions on intestinal stem cells are discussed and, finally, how the production and function of metabolites are modulated by aging and dietary intake is commented upon.     

The Dynamic Distribution of Porcine Microbiota across Different Ages and Gastrointestinal Tract Segments

Metagenome of gut microbes has been implicated in metabolism, immunity, and health maintenance of its host. However, in most of previous studies, the microbiota was sampled from feces instead of gastrointestinal (GI) tract. In this study, we compared the microbial populations from feces at four different developmental stages and contents of four intestinal segments at maturity to examine the dynamic shift of microbiota in pigs and investigated whether adult porcine fecal samples could be used to represent samples of the GI tract. Analysis results revealed that the ratio of Firmicutes to Bacteroidetes from the feces of the older pigs (2-, 3-, 6- month) were 10 times higher compared to those from piglets (1-month). As the pigs matured, so did it seem that the composition of microbiome became more stable in feces. In adult pigs, there were significant differences in microbial profiles between the contents of the small intestine and large intestine. The dominant genera in the small intestine belonged to aerobe or facultative anaerobe categories, whereas the main genera in the large intestine were all anaerobes. Compared to the GI tract, the composition of microbiome was quite different in feces. The microbial profile in large intestine was more similar to feces than those in the small intestine, with the similarity of 0.75 and 0.38 on average, respectively. Microbial functions, predicted by metagenome profiles, showed the enrichment associated with metabolism pathway and metabolic disease in large intestine and feces while higher abundance of infectious disease, immune function disease, and cancer in small intestine. Fecal microbes also showed enriched function in metabolic pathways compared to microbes from pooled gut contents. Our study extended the understanding of dynamic shift of gut microbes during pig growth and also characterized the profiles of bacterial communities across GI tracts of mature pigs.     

Probiotic roles of Lactobacillus sp. in swine: insights from gut microbiota

The use of lactobacilli as probiotics in swine has been gaining attention due to their ability to improve growth performance and carcass quality, prevent gastrointestinal infection and most importantly, their ‘generally recognized as safe’ status. Previous studies support the potential of lactobacilli to regulate host immune systems, enhance gut metabolic capacities and maintain balance in the gut microbiota. Research on swine gut microbiota has revealed complex gut microbial community structure and showed the importance of Lactobacillus to the host's health. However, the species‐ and strain‐specific characteristics of lactobacilli that confer probiotic benefits are still not well understood. The diversity of probiotic traits in a complex gut ecosystem makes it challenging to infer the relationships between specific functions of Lactobacillus sp. and host health. In this review, we provide an overview of how lactobacilli play a pivotal role in the swine gut ecosystem and identify key characteristics that influence gut microbial community structure and the health of pigs. In addition, based on recent and ongoing meta‐omics and omics research on the gut microbiota of pigs, we suggest a workflow combining culture‐dependent and culture‐independent approaches for more effective selection of probiotic lactobacilli.     

Shuttling of information between the mucosal and luminal environment drives intestinal homeostasis

The gastrointestinal tract is a passageway for dietary nutrients, microorganisms and xenobiotics. The gut is home to diverse bacterial communities forming the microbiota. While bacteria and their metabolites maintain gut homeostasis, the host uses innate and adaptive immune mechanisms to cope with the microbiota and luminal environment. In recent years, multiple bi-directional instructive mechanisms between microbiota, luminal content and mucosal immune systems have been uncovered. Indeed, epithelial and immune cell-derived mucosal signals shape microbiota composition, while microbiota and their by-products shape the mucosal immune system. Genetic and environmental perturbations alter gut mucosal responses which impact on microbial ecology structures. On the other hand, changes in microbiota alter intestinal mucosal responses. In this review, we discuss how intestinal epithelial Paneth and goblet cells interact with the microbiota, how environmental and genetic disorders are sensed by endoplasmic reticulum stress and autophagy responses, how specific bacteria, bacterial- and diet-derived products determine the function and activation of the mucosal immune system. We will also discuss the critical role of HDAC activity as a regulator of immune and epithelial cell homeostatic responses.     

Effect of dietary modulation of intestinal microbiota on reproduction and early growth

An optimal balance of intestinal microbiota is necessary for digestive and immune health. Poor performance, susceptibility to infections, and decreased growth rate can be signs of an imbalanced microbiome. Dietary strategies to establish and maintain an optimal balance of microbiota include prebiotics (food for indigenous microbiota in the gastrointestinal tract) and probiotics (beneficial microbiota consumed by the animal). Recent research regarding use of probiotics and prebiotics in reproducing and growing livestock and companion animals is summarized. Documented benefits include prevention of diarrhea, decreased mortality, establishment of a healthy microbiota balance, and improved immune function.     

Impact of selected Lactobacillus and Bifidobacterium species on Listeria monocytogenes infection and the mucosal immune response

The pathogenesis of Listeria monocytogenes depends on its ability to attach to and invade the gastrointestinal epithelium and subsequently withstand the host immune response. Despite a thorough understanding of the intracellular phase of infection, relatively little is known about how the pathogen behaves in the gastrointestinal tract and whether it is affected by the presence of host commensal microbiota. Lactobacillus and Bifidobacterium are two important genera of the human gut microbiota proposed to possess probiotic effects. Here we demonstrate that probiotic bacteria significantly inhibit subsequent listerial infection in an in vitro C2Bbe1 epithelial cell model. In the case of Lactobacilli, inhibition was due to a combination of acid production and secretion of an as yet unidentified protein. In the case of Bifidobacterium, inhibition was attributable to an extracellular proteinaceous secreted compound. In addition, we observed a significant reduction in interleukin-8 and an increase in IL-10 cytokines secreted from epithelial cells following probiotic pretreatment and subsequent infection with Listeria. A reduction in the infection of epithelial cells and an altered mucosal immune response suggests that probiotic bacteria could be of therapeutic benefit against listerial infection. This study infers a role for probiotic bacteria as an antagonist of Li. monocytogenes infection.     

Targeting friend and foe: Emerging therapeutics in the age of gut microbiome and disease

Mucosal surfaces that line our gastrointestinal tract are continuously exposed to trillions of bacteria that form a symbiotic relationship and impact host health and disease. It is only beginning to be understood that the cross-talk between the host and microbiome involve dynamic changes in commensal bacterial population, secretion, and absorption of metabolites between the host and microbiome. As emerging evidence implicates dysbiosis of gut microbiota in the pathology and progression of various diseases such as inflammatory bowel disease, obesity, and allergy, conventional treatments that either overlook the microbiome in the mechanism of action, or eliminate vast populations of microbes via wide-spectrum antibiotics need to be reconsidered. It is also becoming clear the microbiome can influence the body’s response to therapeutic treatments for cancers. As such, targeting the microbiome as treatment has garnered much recent attention and excitement from numerous research labs and biotechnology companies. Treatments range from fecal microbial transplantation to precision-guided molecular approaches. Here, we survey recent progress in the development of innovative therapeutics that target the microbiome to treat disease, and highlight key findings in the interplay between host microbes and therapy.     

Influence of dietary zinc oxide and copper sulfate on the gastrointestinal ecosystem in newly weaned piglets

Dietary doses of 2,500 ppm ZnO-Zn reduced bacterial activity (ATP accumulation) in digesta from the gastrointestinal tracts of newly weaned piglets compared to that in animals receiving 100 ppm ZnO-Zn. The amounts of lactic acid bacteria (MRS counts) and lactobacilli (Rogosa counts) were reduced, whereas coliforms (MacConkey counts) and enterococci (Slanetz counts, red colonies) were more numerous in animals receiving the high ZnO dose. Based on 16S rRNA gene sequencing, the colonies on MRS were dominated by three phylotypes, tentatively identified as Lactobacillus amylovorus (OTU171), Lactobacillus reuteri (OTU173), and Streptococcus alactolyticus (OTU180). The colonies on Rogosa plates were dominated by the two Lactobacillus phylotypes only. Terminal restriction fragment length polymorphism analysis supported the observations of three phylotypes of lactic acid bacteria dominating in piglets receiving the low ZnO dose and of coliforms and enterococci dominating in piglets receiving the high ZnO dose. Dietary doses of 175 ppm CuSO(4)-Cu also reduced MRS and Rogosa counts of stomach contents, but for these animals, the numbers of coliforms were reduced in the cecum and the colon. The influence of ZnO on the gastrointestinal microbiota resembles the working mechanism suggested for some growth-promoting antibiotics, namely, the suppression of gram-positive commensals rather than potentially pathogenic gram-negative organisms. Reduced fermentation of digestible nutrients in the proximal part of the gastrointestinal tract may render more energy available for the host animal and contribute to the growth-promoting effect of high dietary ZnO doses. Dietary CuSO(4) inhibited the coliforms and thus potential pathogens as well, but overall the observed effect of CuSO(4) was limited compared to that of ZnO.     

Probiotic Lactobacillus reuteri biofilms produce antimicrobial and anti-inflammatory factors

Background  

Commensal-derived probiotic bacteria inhibit enteric pathogens and regulate host immune responses in the gastrointestinal tract, but studies examining specific functions of beneficial microbes in the context of biofilms have been limited in scope.     

Diversity,ecology and intestinal function of bifidobacteria

The human gastrointestinal tract represents an environment which is a densely populated home for a microbiota that has evolved to positively contribute to host health. At birth the essentially sterile gastrointestinal tract (GIT) is rapidly colonized by microorganisms that originate from the mother and the surrounding environment. Within a short timeframe a microbiota establishes within the (breastfed) infant's GIT where bifidobacteria are among the dominant members, although their numerical dominance disappears following weaning. The numerous health benefits associated with bifidobacteria, and the consequent commercial relevance resulting from their incorporation into functional foods, has led to intensified research aimed at the molecular understanding of claimed probiotic attributes of this genus. In this review we provide the current status on the diversity and ecology of bifidobacteria. In addition, we will discuss the molecular mechanisms that allow this intriguing group of bacteria to colonize and persist in the GIT, so as to facilitate interaction with its host.     

The gut microbiota,a key to understanding the health implications of micro(nano)plastics and their biodegradation

The effects of plastic debris on the environment and plant, animal, and human health are a global challenge, with micro(nano)plastics (MNPs) being the main focus. MNPs are found so often in the food chain that they are provoking an increase in human intake. They have been detected in most categories of consumed foods, drinking water, and even human feces. Therefore, oral ingestion becomes the main source of exposure to MNPs, and the gastrointestinal tract, primarily the gut, constantly interacts with these small particles. The consequences of human exposure to MNPs remain unclear. However, current in vivo studies and in vitro gastrointestinal tract models have shown that MNPs of several types and sizes impact gut intestinal bacteria, affecting gut homeostasis. The typical microbiome signature of MNP ingestion is often associated with dysbiosis and loss of resilience, leads to frequent pathogen outbreaks, and local and systemic metabolic disorders. Moreover, the small micro- and nano-plastic particles found in animal tissues with accumulated evidence of microbial degradation of plastics/MNPs by bacteria and insect gut microbiota raise the issue of whether human gut bacteria make key contributions to the bio-transformation of ingested MNPs. Here, we discuss these issues and unveil the complex interplay between MNPs and the human gut microbiome. Therefore, the elucidation of the biological consequences of this interaction on both host and microbiota is undoubtedly challenging. It is expected that microbial biotechnology and microbiome research could help decipher the extent to which gut microorganisms diversify and MNP-determinant species, mechanisms, and enzymatic systems, as well as become important to understand our response to MNP exposure and provide background information to inspire future holistic studies.