Differences in Microbiota Membership along the Gastrointestinal Tract of Piglets and Their Differential Alterations Following an Early-Life Antibiotic Intervention

Selective Regional Alteration of the Gut Microbiota by Diet and Antibiotics

The small intestinal microbiota has recently been implicated in contributing to metabolic disease. We previously demonstrated that diets rich in saturated milk fat have a particularly strong impact on the small bowel microbiota as opposed to more distal gastrointestinal (GI) regions. However, the impact of antibiotics and diet on the small bowel microbiota has not been clearly demonstrated. Thus, we sought to determine how diet and antibiotics interact in modulating the regional landscape of the gut microbiota. We conducted a study using male mice on a high fat (HF) or a low fat (LF) diet (n = 15/group) that received either water control (n = 5/diet), rifaximin, (non-absorbable broad-spectrum antibiotic; n = 5/diet) or an antibiotic cocktail consisting of metronidazole, cefoperazone, vancomycin, and neomycin (Abx cocktail; n = 5/diet). 16S rRNA sequencing was performed on mucosal scrapings collected from the small intestine and cecum, as well as on stool samples. Interestingly, antibiotics had a significant effect on community composition throughout the small intestine, cecum and stool, whereas diet significantly affected only the jejunum and cecum microbiota. The antibiotic cocktail, regardless of diet, was most effective in increasing cecum size, reducing body fat percentage, and plasma lipid levels. Altogether, this study reveals a selective and divergent regional alteration of the gut microbiota by diet and antibiotics.

Effect of early antibiotic intervention on specific bacterial communities and immune parameters in the small intestine of growing pigs fed different protein level diets

Antibiotics are designed to affect gut microbiota and subsequently gut homeostasis. However, limited information exists about short- and long-term effects of early antibiotic intervention (EAI) on gut homeostasis (especially for the small intestine) of pigs following antibiotic withdrawal. We investigated the impact of EAI on specific bacterial communities, microbial metabolites and mucosal immune parameters in the small intestine of later-growth-stage pigs fed with diets differing in CP levels. Eighteen litters of piglets were fed creep feed with or without antibiotics from day 7 to day 42. At day 42, pigs within each group were offered a normal- or low-CP diet. Five pigs per group were slaughtered at days 77 and 120. At day 77, EAI increased Enterobacteriaceae counts in the jejunum and ileum and decreased Bifidobacterium counts in the jejunum and ileum (P < 0.05). Moreover, tryptamine, putrescine, secretory immunoglobulin (Ig) A and IgG concentrations in the ileum and interleukin-10 (IL-10) mRNA and protein levels in the jejunum and ileum were decreased in pigs with EAI (P < 0.05). At day 120, EAI only suppressed Clostridium cluster XIVa counts in the jejunum and ileum (P < 0.05). These results suggest that EAI has a short-term effect on specific bacterial communities, amino acid decarboxylation and mucosal immune parameters in the small intestine (particularly in the ileum). At days 77 and 120, feeding a low-CP diet affected Bifidobacterium, Clostridium cluster IV, Clostridium cluster XIVa and Enterobacteriaceae counts in the jejunum or ileum (P < 0.05). Moreover, feeding a low-CP diet increased the concentrations of Igs in the jejunum and decreased pro-inflammatory cytokines levels in the jejunum and ileum (P < 0.05). At day 120, feeding a low-CP diet increased short-chain fatty acid concentrations, reduced ammonia and spermidine concentrations and up-regulated genes related to barrier function in the jejunum and ileum (P < 0.05). These results suggest that feeding a low-CP diet changes specific bacterial communities and intestinal metabolite concentrations and modifies mucosal immune parameters. These findings contribute to our understanding on the duration of the impact of EAI on gut homeostasis and may provide basis data for nutritional modification in young pigs after antibiotic treatment.

Tryptophan Metabolism: A Link Between the Gut Microbiota and Brain

The gut-brain axis (GBA) is a bilateral communication network between the gastrointestinal (GI) tract and the central nervous system. The essential amino acid tryptophan contributes to the normal growth and health of both animals and humans and, importantly, exerts modulatory functions at multiple levels of the GBA. Tryptophan is the sole precursor of serotonin, which is a key monoamine neurotransmitter participating in the modulation of central neurotransmission and enteric physiological function. In addition, tryptophan can be metabolized into kynurenine, tryptamine, and indole, thereby modulating neuroendocrine and intestinal immune responses. The gut microbial influence on tryptophan metabolism emerges as an important driving force in modulating tryptophan metabolism. Here, we focus on the potential role of tryptophan metabolism in the modulation of brain function by the gut microbiota. We start by outlining existing knowledge on tryptophan metabolism, including serotonin synthesis and degradation pathways of the host, and summarize recent advances in demonstrating the influence of the gut microbiota on tryptophan metabolism. The latest evidence revealing those mechanisms by which the gut microbiota modulates tryptophan metabolism, with subsequent effects on brain function, is reviewed. Finally, the potential modulation of intestinal tryptophan metabolism as a therapeutic option for brain and GI functional disorders is also discussed.

The gut-eye-lacrimal gland-microbiome axis in Sjögren Syndrome

The bacterial communities that collectively inhabit our body are called the microbiome. Virtually all body surface harbors bacteria. Recent advances in next-generation sequencing that have provided insight into the diversity, composition of bacterial communities, and their interaction are discussed in this review, as well as the current knowledge of how the microbiome promotes ocular health. The ocular surface is a site of low bacterial load. Sjögren Syndrome is an autoimmune disease that affects the exocrine glands, causing dry mouth and dry eye. Systemic antibiotic treatment and germ-free mice have demonstrated that commensal bacteria have a protective role for the ocular surface and lacrimal gland. The existence of a gut-eye-lacrimal gland axis-microbiome is discussed.

Effects of Three Distinct 2-Week Long Diet Strategies After Transport on Weaned Pigs' Short and Long-Term Welfare Markers, Behaviors, and Microbiota

Alternative feed supplements have shown promising effects in terms of performance, but their effects on welfare have had little evaluation. In the present study, we aimed at evaluating the effect of diet supplementation on welfare indicators. A total of 246 piglets were weaned and transported for 12 h. After transport, they were assigned to one of 3 diets for a 14-day period: A-an antibiotic diet including chlortetracycline and tiamulin, NA-a control diet without any antibiotic or feed supplement, GLN-a diet including 0.20% L-glutamine. After the 14-day period, all piglets were fed the same diet. Tear staining was measured 11 times post-weaning (from d0 to 147). Skin lesions were counted before and after weaning (d-2, 2, and 36). Novel object tests (NOT) were done in groups 4 times post-weaning (d17, 47, 85, 111). Samples for 16S rRNA gene composition were collected prior to transport (d0), following the 14-day period (d14) and at the conclusion of the nursery phase (d34). The NA pigs appeared less interested in novel objects. On d17, they avoided the object less than A pigs (P < 0.05). They spent less time exploring the object on d85 and took longer to interact with the object on d111 than A and GLN pigs (P < 0.05). NA pigs also appeared more sensitive to environment and management. They had larger tear stains than GLN pigs on d84 and 110 (P < 0.05). On d2, NA pigs had more lesions than A and GLN (P < 0.01). In terms of microbiota composition, GLN had higher α-diversity than A and NA (P < 0.001). Differences between dietary treatments were absent at d0, were demonstrated at d14 and disappeared at d34. Pearson correlations between aggression, stress and anxiety indicators and bacterial populations were medium to high from 0.31 to 0.69. The results demonstrate that short-term feeding strategy can have both short- and long-term effects on behavior and welfare, that may partly be explained by changes in gut microbiota composition. Supplementation with GLN appears to confer similar benefits to dietary antibiotics and thus could be a viable alternative.

The microbiota and immune-mediated diseases: Opportunities for therapeutic intervention

A multitude of diverse microorganisms, termed the microbiota, reside in the gut, respiratory tract, skin, and genital tract of humans and other animals. Recent advances in metagenomic sequencing and bioinformatics have enabled detailed characterization of these vital microbial communities. Studies in animal models have uncovered vital previously unrecognized roles for the microbiota in normal function of the immune responses, and when perturbed, in the pathogenesis of diseases of the gastrointestinal tract and lungs, but also at distant sites in the body including the brain. The composition of gut and respiratory microbiota can influence systemic inflammatory responses that mediate asthma, allergy, inflammatory bowel disease, obesity-related diseases, and neurodevelopmental or neurodegenerative conditions. Experiments in mouse models as well as emerging clinical studies have revealed that therapeutic manipulation of the microbiota, using fecal microbiota transplantation, probiotics, or engineered probiotics represent effective nontoxic approaches for the treatment or prevention of Clostridium difficile infection, allergy, and autoimmune diseases and may enhance the efficacy of certain cancer immunotherapeutics. This review discusses how commensal bacteria can influence immune responses that mediate a range of human diseases and how the microbiota are being targeted to treat these diseases, especially those resistant to pharmacological therapies.

Early Parenteral Administration of Ceftiofur has Gender-Specific Short- and Long-Term Effects on the Fecal Microbiota and Growth in Pigs from the Suckling to Growing Phase

Simple Summary

Antibiotics are commonly used in prevention and therapy of bacterial diseases in pig production. Although the main target of antibiotics are the pathogenic bacteria, they often disrupt the commensal gut microbiota as a whole, leading to intestinal disturbances. These detrimental effects have been well established for oral administration of antibiotics, whereas knowledge about potential disturbing effects of single parenteral antibiotic treatments on the gut microbiota development is limited. In this research, the impact of a single antibiotic injection on the first day of life on the maturation of the fecal microbiome and host growth performance was evaluated from the suckling to the growing phase. Results showed that a single antibiotic injection early in life influenced the bacterial community development in the short- and long-term and that this disturbance in the bacterial community was sex-specific. Present results further demonstrated that changes in the bacterial ecosystem of the gut may impair the growth performance of the growing pig. Thus, the results of the present study emphasize the importance of a proper and strict use of antibiotics in swine herds.

Abstract

Using ceftiofur during the first days of life is a common preventative strategy against several bacterial diseases in pig production. This study aimed to evaluate short- and long-term effects of early use of ceftiofur on the fecal microbiota development in suckling and growing pigs. Sixty-four piglets from eight litters were assigned to the antibiotic (AB; n = 32) or control group (control; n = 32). Twelve hours postpartum (day 0) AB piglets received an intramuscular injection of ceftiofur (5.0 mg/kg body weight) or a placebo. DNA was extracted from fecal samples collected on days 0, 12, 28, and 97 for deep-sequencing of the 16S rRNA gene. The AB administration disturbed the maturational changes in the fecal microbiome, whereby effects were sex-specific. Sex-related differences in AB metabolism in females and males may have caused these diverging AB-effects on the fecal microbiota. Especially the loss of bacterial diversity and of certain taxa in female AB pigs may have contributed to the decreased body weight of these females on day 97 of life. Taken together, this study showed that an AB injection with ceftiofur 12 h postpartum markedly affected the successional changes in the fecal microbiota composition in male and female pigs, with long-term consequences for host performance.

Antibiotic effects on gut microbiota, metabolism, and beyond

Current advances on gut microbiota have broadened our view on host-microbiota interactions. As a microbiota-targeted approach, the use of antibiotics has been widely adopted to explore the role of gut microbiota in vivo. Antibiotics can change the microbial composition, resulting in varied effects, depending on the antibiotic class, dosage, and duration. Antibiotic intervention in early life leads to life-long phenotype alterations, including obesity. Antibiotic-induced changes in gut microbiota affect the epithelial utilization of both macronutrients (e.g., amino acids) and micronutrients (e.g., copper, vitamin E) and the redox homeostasis. Of particular interest is the regulation of gut anaerobiosis and aerobiosis by oxygen availability, which is closely related to epithelial metabolism. Additionally, antibiotic interventions enable to identify novel roles of gut microbiota in gut-liver axis and gut-brain axis. Indigenous antimicrobial molecules are produced by certain microbes, and they have the potential to affect function through eliciting changes in the gut microbiota. This review discusses at length these findings to gain a better and novel insight into microbiota-host interactions and the mechanisms involved.

Microbiota Composition and Functional Profiling Throughout the Gastrointestinal Tract of Commercial Weaning Piglets

Dietary, environmental, and social stresses induced by weaning transition in pig production are associated with alterations of gut microbiota, diarrhea, and enteric infections. With the boom of -omic technologies, numerous studies have investigated the dynamics of fecal bacterial communities of piglets throughout weaning but much less research has been focused on the composition and functional properties of microbial communities inhabiting other gastrointestinal segments. The objective of the present study was to bring additional information about the piglet bacterial and archaeal microbiota throughout the entire digestive tract, both at the structural level by using quantitative PCR and high-throughput sequencing, and on functionality by measurement of short-chain fatty acids and predictions using Tax4Fun tool. Our results highlighted strong structural and functional differences between microbial communities inhabiting the fore and the lower gut as well as a quantitatively important archaeal community in the hindgut. The presence of opportunistic pathogens was also noticed throughout the entire digestive tract and could trigger infection emergence. Understanding the role of the intestinal piglet microbiota at weaning could provide further information about the etiology of post-weaning infections and lead to the development of effective preventive solutions.

Grape Seed Proanthocyanidin Affects Lipid Metabolism via Changing Gut Microflora and Enhancing Propionate Production in Weaned Pigs

BACKGROUND

It is not clear whether dietary grape seed proanthocyanidin (GSP) affects mammalian lipid metabolism via the gut microbiota.

OBJECTIVE

The aim of this study was to evaluate the contribution of the gut microbiota to the effect of dietary GSP.

METHODS

This study was divided into 3 separate experiments using Duroc × Landrace × Yorkshire pigs (50% male) weaned at day 28 and then fed the same basal diet (NC). In Experiment 1, 90 pigs were fed NC or NC with 250 mg GSP/kg (GSP) or 400 mg betaine/kg [positive control (PC)] for 28 d. In Experiment 2, 30 pigs were fed NC, GSP, or GSP with antibiotics (GSP + Abx) diets for 14 d. In Experiment 3, pigs were fed NC, NC plus 1 g sodium propionate/kg (SP), or NC plus 1 g sodium butyrate/kg (SB) diet for 14 d. Serum biochemical indexes, SCFA concentrations, and microbial composition were determined.

RESULTS

In Experiment 1, compared with the GSP group, visceral adipocyte area was higher in the NC (28.6%) and PC (18.2%) groups (P ≤ 0.05). Colonic propionate and butyrate concentrations were 30.2% and 3.6% higher in the GSP group than in the NC group, respectively (P ≤ 0.05). In Experiment 2, compared with the GSP group, the NC group had a 108% higher Firmicutes to Bacteroidetes ratio and had 50.4%, 61.2%, and 82.3% lower abundance of Akkermansia, Alistipes, and Bacteroides, respectively (P ≤ 0.05); antibiotics removed these effects of GSP. In Experiment 3, serum peptide YY was 19.5% higher in the SP group than in the NC group (P ≤ 0.05), and it did not differ between the SB and NC groups (P > 0.05).

CONCLUSIONS

GSP affected lipid metabolism in weaned pigs, which is associated with changed gut microbiota and enhanced microbial propionate production. These findings provide potential mechanisms for GSP intake to improve lipid metabolism.

Legitimate and Reliable Determination of the Age-Related Intestinal Microbiome in Young Piglets; Rectal Swabs and Fecal Samples Provide Comparable Insights

A prerequisite for reliable microbiota analysis is having an effective and consistent sampling method. Fecal sampling, commonly used to study the intestinal microbiome, might not be suitable in all situations, especially considering the potential difficulties in obtaining fresh feces from young animals. Indeed, this study shows that the success rate of collecting fecal samples from young piglets (<2 weeks of age) was very low. Therefore, we evaluated rectal swabs as an alternative sample type (to feces) for studying porcine microbiome development and performed a comparative analysis of microbiome composition obtained from fresh fecal samples and rectal swabs in 15 healthy piglets at seven (6 piglets) and 20 (9 piglets) days of age. Three samples (fresh feces, rectal swab before and after defecation) were collected from individual piglets and microbiome composition was assessed by 16S rRNA gene sequencing. The results demonstrated that rectal swabs and fecal samples provide similar microbiome composition profiles, with samples clustering predominantly by individual animal rather than sample type. Furthermore, regardless of the sample type, the biological interpretation with respect to microbiota colonization patterns associated with different ages (7 and 20 days) was found to be comparable. Independent of sample type, we observed age-related changes like increasing microbiota diversity and alterations in relative abundances of the phyla Firmicutes, Bacteroidetes, and Fusobacteria, which was also reflected in consistent family- and genus-level microbiota changes. This study establishes that rectal swabs are a suitable alternative sample type to study the porcine microbiome development in early life, when fecal sampling is challenging.

Synbiotics impact on dominant faecal microbiota and short-chain fatty acids production in sows

The aim of this study was to estimate the influence of synbiotics on intestinal microbiota and its metabolism in sows. Three different synbiotics were administered with feed to animals from three experimental groups. Two groups of sows were given commercially available probiotics (BioPlus 2B®, Cylactin® LBC) as forage additives for comparison. The control group of sows was given unmodified fodder. The study was conducted for 48 days (10 days before farrowing, and continued 38 days after) and faeces samples were collected four times. The scope of this work was to designate the dominant microbiota in sows' faeces. Therefore, the total number of anaerobic bacteria, Bifidobacterium sp., Lactobacillus sp., Bacteroides sp., Clostridium sp., Enterococcus sp., Enterobacteriaceae, Escherichia coli and yeast was determined, using the plate method. Changes in the concentration of lactic acid, short-chain fatty acids (SCFAs) and branched-chain fatty acids (BCFAs) were also determined in correlation with the feed additives administered to the sows using high-performance liquid chromatography analysis (HPLC). Our results allowed us to conclude that synbiotics have a beneficial effect on intestinal microbiota of sows and its metabolism. We observed that the impact of the synbiotics on the microbiota was more significant than the one induced by probiotics.

Antimicrobial Effects on Swine Gastrointestinal Microbiota and Their Accompanying Antibiotic Resistome

Antimicrobials are the most commonly prescribed drugs in the swine industry. While antimicrobials are an effective treatment for serious bacterial infections, their use has been associated with major adverse effects on health. It has been shown that antimicrobials have substantial direct and indirect impacts on the swine gastrointestinal (GI) microbiota and their accompanying antimicrobial resistome. Antimicrobials have also been associated with a significant public health concern through selection of resistant opportunistic pathogens and increased emergence of antimicrobial resistance genes (ARGs). Since the mutualistic microbiota play a crucial role in host immune regulation and in providing colonization resistance against potential pathogens, the detrimental impacts of antimicrobial treatment on the microbiota structure and its metabolic activity may lead to further health complications later in life. In this review, we present an overview of antimicrobial use in the swine industry and their role in the emergence of antimicrobial resistance. Additionally, we review our current understanding of GI microbiota and their role in swine health. Finally, we investigate the effects of antimicrobial administration on the swine GI microbiota and their accompanying antibiotic resistome. The presented data is crucial for the development of robust non-antibiotic alternative strategies to restore the GI microbiota functionality and guarantee effective continued use of antimicrobials in the livestock production system.

Diversity and community pattern of sulfate-reducing bacteria in piglet gut

Background

Among the gut microbiota, sulfate-reducing bacteria (SRB) is a kind of hydrogen-utilizing functional bacteria that plays an important role in intestinal hydrogen and sulfur metabolism. However, information is lacking regarding diversity and community structure of SRB in the gut of piglets. Middle cecum contents were collected from 6 Yorkshire and 6 Meishan piglets at postnatal days (PND) 14, 28 and 49. Piglets were weaned at PND28. Real-time quantitative PCR was performed to detect the number of SRB in the cecum based on dissimilatory sulfite reductase subunit A (dsrA) gene. Prior to real-time PCR, plasmid containing the dsrA gene was constructed and used as external standard to create a standard curve, from which the gene copies of dsrA were calculated. H₂S concentration in the cecal contents was measured. Illumina PE250 sequencing of dsrA gene was used to investigate SRB diversity in cecum contents.

Results

The qPCR results showed that the number of SRB at PND49 was significantly higher than that at PND28 in Meishan piglets. The concentration of H₂S has no significant difference between piglet breeds and between different ages. The Illumina sequencing analysis revealed that the Chao1 richness index was significantly higher at PND49 than that at PND14 and PND28 in Yorkshire piglets. Based on dsrA gene similarities, Proteobacteria, Actinobacteria, and Firmicutes were identified at the phylum level, and most sequences were classified as Proteobacteria. At the genus level, most of sequences were classified as Desulfovibrio. At the species level, Desulfovibrio intestinalis was the predominant SRB in the piglet cecum. The relative abundance and the inferred absolute abundance of Faecalibacterium prausnitzii at PND49 were significantly higher than that at PND14 in Yorkshire piglets. Pig breeds did not affect the dsrA gene copies of SRB, diversity index and community pattern of SRB.

Conclusions

Sulfate-reducing bacteria are widely colonized in the cecum of piglets and D. intestinalis is the dominant SRB. The age of piglets, but not the pig breeds affects the diversity and community pattern of SRB.

Electronic supplementary material

The online version of this article (10.1186/s40104-019-0346-5) contains supplementary material, which is available to authorized users.

Succession of organics metabolic function of bacterial community in response to addition of earthworm casts and zeolite in maize straw composting

Succession and metabolism functions of bacterial communities were determined in maize straw composting with earthworm casts and zeolite addition by using high-throughput sequencing, Biolog and PICRUSt. Results showed that earthworm casts and zeolite addition increased the temperature, decreased NH₄⁺ contents and affected bacterial community structure. The relative abundances of Firmicutes and Betaproteobacteria increased with earthworm casts and zeolite addition in the late stage. The abundances of genes related to carbohydrate metabolism, amino acid metabolism, and energy metabolism were increased by these two additives in the early stage, but decreased in the late stage. Network analysis demonstrated that members of Bacillaceae were identified as the keystone taxa. Temperature showed negative relationship with Georgenia, while NH₄⁺ exhibited positive associations with Georgenia, Devosia, Ruania and Mycobacterium. These results indicated that earthworm casts and zeolite addition benefitted the keystone species and enhanced the metabolism capacity of bacterial community, thereby improved the quality of compost.

Differential Effects of Breed and Nursing on Early-Life Colonic Microbiota and Immune Status as Revealed in a Cross-Fostering Piglet Model

Nursing mother and breed can differently regulate early-life microbiota succession in pigs. However, it remains unclear whether they affect gastrointestinal microbiota and immune status, which are critical for early-life gut health. Here, an interspecific cross-fostering piglet model was employed by fostering neonatal Yorkshire and Meishan piglets to the same or another breed of sows. Jejunal and colonic microbiotas and mucosal immune parameters were analyzed at postnatal days 14 (preweaning) and 49 (postweaning). Nursing mother affected 10 genera in the colon and 3 minor genera in the jejunum. At day 14, Meishan sow-nursed piglets had lower Streptococcus suis and higher Cloacibacillus counts in the colonic digesta and larger amounts of interleukin 10 and Foxp3-positive cells in the colonic mucosa than did Yorkshire sow-nursed piglets. At day 49, nursing mother had no significant effects on cytokine expression. Breed effects were observed; Meishan piglets had lower relative abundances of Prevotella and lower gene expression of tumor necrosis factor alpha (TNF-α) than those of Yorkshire piglets at days 14 and 49. Collectively, nursing mother mainly affected preweaning colonic microbiota and immune status, while breed effects persisted after weaning. Piglets nursed by Meishan sows had different microbiota compositions and inflammatory cytokine profiles in the colon compared with those of piglets nursed by Yorkshire sows. These results highlight the different role of nursing mother and breed in affecting early gut microenvironment.IMPORTANCE Early-life gut microbiota and immune status are pivotal for postnatal growth. By using an interspecific cross-fostering piglet model, we find that change in nursing mother transiently reshapes preweaning colon microbiota and immune status, while breed shows persistent effects both pre- and postweaning. Piglets nursed by Meishan sows had lower Streptococcus suis counts and higher anti-inflammatory cytokine expression. These results highlight the significance of nursing mother in regulating early-life gut health.

Characterization of the Early Life Microbiota Development and Predominant Lactobacillus Species at Distinct Gut Segments of Low- and Normal-Birth-Weight Piglets

Microbial exposure during early life plays a pivotal role in modulating the health and intestinal development of the host. Our recent study showed that the low-birth-weight (LBW) piglets harbored a different fecal microbiota compared to normal-birth-weight (NBW) piglets during early life with a lower abundance of the genus Lactobacillus. Considering the spatial variations in gut microbiota at distinct gut locations, this study was designed to further investigate the differences in the microbiota composition and predominant Lactobacillus species in the ileum and colon between LBW and NBW piglets during early life, including day 7 (D7), day 21 (D21, before weaning), and day 35 (D35, 2 weeks after weaning). Compared with the normal group, LBW piglets harbored a significantly lower proportion of short-chain fatty acids producing microbes, such as Ruminococcaceae and Prevotellaceae in the ileum on D7, Alistipes and Lachnospiraceae in the colon on D7, Blautia in the colon on D21, and Ruminiclostridium 9 in the colon on D35. The relative abundance of the phylum Bacteroidetes was also declined in both ileum and colon of LBW piglets on D7. Meanwhile, the levels of total SCFAs on D7, D21, and D35, acetate and valerate on D7 and D21, propionate on D21, and lactate on D21 and D35, were also declined in the colon of LBW piglets. Moreover, functional alterations in the gut microbiota of LBW piglets were characterized by differentially abundant microbial genes involved in multiple pathways such as amino acid metabolism, energy metabolism, replication and repair, and metabolism of cofactors and vitamins in the colon. Additionally, lower numbers of L. salivarius on D7 and L. amylovorus on D21 resided in the colon of LBW piglets compared to those in the normal ones. Collectively, LBW piglets have altered bacterial communities, microbial metabolism and gene functions in the ileum and colon during early life, especially the colonic community. This work will help to develop novel ideas in identifying the reliable biomarkers affecting the gut microbiota development in LBW piglets during early life and facilitate the development of new nutritional interventions.

Characterization of Microbiota Associated with Digesta and Mucosa in Different Regions of Gastrointestinal Tract of Nursery Pigs

Weaning is a crucial period when piglets have to cope with sudden dietary, social, and environmental stressors that often lead to serious intestinal dysbiosis and mortality. In this study, five mucosal and five digesta samples from each proximate jejunum, distal jejunum, and mid-colon were collected from 7- and 27-day post-weaned pigs and subjected to microbiota analysis using 16S rRNA gene profiling. Taxonomic analysis at phylum level revealed that Proteobacteria was significantly higher at 7 days (13.54%), while Bacteriodetes was higher at 27 days (30.72%) post weaning. Genera such as Campylobacter, Veillonella, Helicobacter, and Blautia that were previously reported in intestinal dysbiosis were significantly enriched in seven-day post-weaned pigs. However, microbial communities shifted as post weaning age increased with a significant increase in alpha diversity, and genera such as Moryella, Dialister, Clostridium, Streptococcus, Prevotella, and Bacteroides become significantly abundant in 27-day post-weaned pigs. Interestingly, the genus Campylobacter was significantly abundant on seven-day post-weaning in two piglets with diarrhea, implicating its role in post-weaning diarrhea. The results of this study suggest that gut microbiota in pigs with dysbiosis on 7-day post weaning undergoes significant changes toward a more normal state as the post-weaning age reaches 27 days.

Effects of dietary supplementation of probiotic Enterococcus faecium on growth performance and gut microbiota in weaned piglets

The adverse effects of antibiotics have attracted widespread attention, thus reducing the use of antibiotics in animal feed has become a very important issue in improving of the health of livestock. The effects of Enterococcus faecium (E. faecium) on growth performance and gut microbiota in weaned piglets were investigated in the present study. Piglets were randomly assigned to four treatments: a control group fed with a diet containing 75 mg/kg aureomycin (Diet 1 group) and three experimental groups fed with diets of 50 mg/kg aureomycin (Diet 2 group), 50 mg/kg aureomycin + 9 × 10⁵ CFU/g E. faecium (Diet 3 group), or 50 mg/kg aureomycin + 1.2 × 10⁶ CFU/g E. faecium (Diet 4 group). Their gut microbial communities were analyzed by sequencing the V3–V4 region of the 16SrRNA gene. The results showed that the final body weights and the average daily gain of the weaned piglets in the Diet 2 group were higher (P = 0.05) than those in the Diet 1 or Diet 3 group. Decreasing trends (P = 0.08) was observed in mortality rate in the Diet 3 and 4 group when compared with that in the Diet 1 group. Increases in the Sobs, Chao1, ACE, and Shannon indexes and a decrease in the Simpson index were observed at intervals from day 1 to 14 (P < 0.05). The Sobs, Chao1, and ACE indexes in the Diet 3 group were the lowest on day 14 (P < 0.05). The abundance of Bacteroidetes was increased and that of Proteobacteria was decreased from day 1 to 7, but both of them kept stable from day 7 to 14. Besides, the lowest abundance of Fusobacteria, Lentisphaerae, and Planctomycetes was observed on day 1 and the lowest abundance of Actinobacteria was observed on day 14 in the Diet 3 group (P < 0.05). Overall, these results suggest that the antibiotics and E. faecium interventions result in different changes in the gut microbiota, and a reduced antibiotics diet supplemented with 1.2 × 10⁶ CFU/g E. faecium does not affect the growth performance in weaned piglets.

The Ovotransferrin-Derived Peptide IRW Attenuates Lipopolysaccharide-Induced Inflammatory Responses

IRW (Ile-Arg-Trp), a bioactive peptide isolated from egg ovotransferrin, has been shown to exert anti-inflammatory effects. In this study, the effects of IRW on inflammatory cytokines and microbiota were explored in human umbilical vein endothelial cells (HUVECs) and a lipopolysaccharide (LPS)-induced rat model of inflammatory peritonitis. Rats were injected intraperitoneally with LPS to establish peritonitis. HUVECs were exposed to IRW for 12 h before introducing LPS. Notably, IRW exerted beneficial effects against LPS-induced peritonitis, specifically, by reducing the serum levels of tumour necrosis factor (TNF)-α and interleukin (IL)-6 and myeloperoxidase (MPO) activity (P<0.05). A faecal microbiota analysis revealed that IRW significantly increased the Shannon and decreased the Simpson indices (P<0.05). Furthermore, IRW treatment significantly inhibited the LPS-induced enhancement of TNF-α, IL-8, intercellular cell adhesion molecule-1 (ICAM-1), and vascular cell adhesion molecule-1 (VCAM-1) expression in HUVECs (P<0.05). In conclusion, IRW supplementation inhibited the inflammatory mediator synthesis and LPS-induced inflammatory responses and influenced the gut microbiota.

Characteristics of gut microbiota and its response to a Chinese Herbal Formula in elder patients with metabolic syndrome

Alterations in gut microbiota have been known to play a critical role in metabolic syndrome. However, the microbial features in elderly patients with metabolic syndrome remain unclear. A traditional Chinese Herbal Formula, Yangyin Tiluo Decoction (YTD), can alleviate metabolic syndrome and cardiovascular disease. To characterize gut microbiota in elder patients and effects of YTD on gut microbiota during treatment of metabolic syndrome, 11 healthy elderly persons and 12 elderly persons (aged 60-90 years) with metabolic syndrome were enrolled. The patients were randomly assigned to receive YTD for 4 weeks (200 mL of the decoction two times daily). The microbial composition in healthy control, pre- and post- YTD treatment group were analyzed by 16S rRNA sequencing of fecal DNAs. Biochemical measurements were conducted for elderly patients. The results showed a high inter-individual variation of gut microbiota in elderly persons. The gut microbiota was dominated by phylum Firmicutes and Actinobacteria, which was distinct from the previously defined microbiota in Irish elderly persons. The elderly patients with metabolic syndrome had higher proportions of Lactobacillus and Bifidobacterium, and lower proportions of Anaerostipes, Coprococcus, Ruminococcus than healthy controls. YTD treatment reduced the abundance of genus Bacteroidales Incertae Sedis and species Enterobacteriaceae Incertae Sedis. The concentration of plasma lipoprotein (a) was also reduced, which was negatively correlated with the abundance of an Acinetobacter species. These results reveal a remarkable dominance of Firmicutes and Actinobacteria, and highlight the distinct gut microbiota in elderly patients with metabolic syndrome, which may be involved in pathogenesis. Furthermore, the benefits of YTD treatment were observed, providing an approach to improve metabolic syndrome in elderly patients.

Effects of Early Intervention with Maternal Fecal Microbiota and Antibiotics on the Gut Microbiota and Metabolite Profiles of Piglets

We investigated the effects of early intervention with maternal fecal microbiota and antibiotics on gut microbiota and the metabolites. Five litters of healthy neonatal piglets (Duroc × Landrace × Yorkshire, nine piglets in each litter) were used. Piglets in each litter were orally treated with saline (CO), amoxicillin treatment (AM), or maternal fecal microbiota transplantation (MFMT) on days 1–6, with three piglets in each treatment. Results were compared to the CO group. MFMT decreased the relative abundances of Clostridium sensu stricto and Parabacteroides in the colon on day 7, whereas the abundance of Blautia increased, and the abundance of Corynebacterium in the stomach reduced on day 21. AM reduced the abundance of Arcanobacterium in the stomach on day 7 and reduced the abundances of Streptococcus and Lachnoclostridium in the ileum and colon on day 21, respectively. The metabolite profile indicated that MFMT markedly influenced carbohydrate metabolism and amino acid (AA) metabolism on day 7. On day 21, carbohydrate metabolism and AA metabolism were affected by AM. The results suggest that MFMT and AM discriminatively modulate gastrointestinal microflora and alter the colonic metabolic profiles of piglets and show different effects in the long-term. MFMT showed a location-specific influence on the gastrointestinal microbiota.

Probiotics-fermented Massa Medicata Fermentata ameliorates weaning stress in piglets related to improving intestinal homeostasis

Weaning stress has serious negative effects on piglets' health and the swine industry. Probiotics-fermented Chinese herbal medicines are potential feed additives to ameliorate weaning stress. In this study, the effects of probiotics-fermented Massa Medicata Fermentata (MMFP) on intestinal homeostasis were evaluated in weaning piglets. Dietary supplementation with MMFP promoted the development of the intestinal structure and elevated the concentrations of lactic acid and short-chain fatty acids (SCFAs) in the intestinal contents and antioxidant capacities in serum. MMFP reduced the levels of inflammatory factors in the intestinal mucosa. Microbial community analysis demonstrated that MMFP led to the selective and progressive enrichment of lactic acid- and SCFA-producing bacteria along the gastrointestinal tract, in particular, OTUs corresponding to Lactobacillus, Streptococcus, Acetitomaculum, Roseburia, and Eubacterium xylanophilum group, while MMFP reduced the relative abundance of pathogenic bacteria. On the contrary, antibiotics had negative effects on intestinal histology and increased the relative abundance of pro-inflammatory bacterium, such as Marvinbryantia, Peptococcus, Turicibacter, and Blautia. Correlation analysis reflected that the bacteria enriched in MMFP group were positively correlated with enhanced intestinal homeostasis, which suggested that dietary supplementation with MMFP enhanced host intestinal homeostasis by modulating the composition of gut microbiota and the levels of beneficial SCFAs, thus ameliorating weaning stress in piglets.

Succession of organics metabolic function of bacterial community in swine manure composting

Organics metabolic function of bacterial communities was evaluated in 60 days composting of swine manure and pumice by using MiSeq sequencing, PICRUSt and Biolog tools. The diversity of bacterial communities significantly decreased during the first 10 days, and gradually increased in the cooling and curing phase. The PICRUSt and Biolog analysis indicated that carbohydrate, lipid and amino acids metabolisms were relatively higher in the thermophilic phases. Xenobiotics biodegradation and metabolism, lipid metabolism, terpenoids and polyketides and biosynthesis of other secondary metabolites were mainly detected in the curing phases. Canonical correspondence analysis (CCA) indicated that the succession of bacterial community and organics utilization characteristics were highly affected by the temperature, moisture and oxidation reduction potential (ORP) in the swine composting system.

How Can We Define "Optimal Microbiota?": A Comparative Review of Structure and Functions of Microbiota of Animals, Fish, and Plants in Agriculture

All multicellular organisms benefit from their own microbiota, which play important roles in maintaining the host nutritional health and immunity. Recently, the number of studies on the microbiota of animals, fish, and plants of economic importance is rapidly expanding and there are increasing expectations that productivity and sustainability in agricultural management can be improved by microbiota manipulation. However, optimizing microbiota is still a challenging task because of the lack of knowledge on the dominant microorganisms or significant variations between microbiota, reflecting sampling biases, different agricultural management as well as breeding backgrounds. To offer a more generalized view on microbiota in agriculture, which can be used for defining criteria of “optimal microbiota” as the goal of manipulation, we summarize here current knowledge on microbiota on animals, fish, and plants with emphasis on bacterial community structure and metabolic functions, and how microbiota can be affected by domestication, conventional agricultural practices, and use of antimicrobial agents. Finally, we discuss future tasks for defining “optimal microbiota,” which can improve host growth, nutrition, and immunity and reduce the use of antimicrobial agents in agriculture.

Response of Gut Microbiota to Dietary Fiber and Metabolic Interaction With SCFAs in Piglets

Dietary fiber (DF) is increasingly thought to regulate diversity of piglet gut microbiota to alleviate weaning stress in piglets. This study was conducted to investigate the effects of DF on growth performance of piglets and composition of their gut microbiota, as well as the interaction between gut microbiota and short-chain fatty acids (SCFAs) in piglets. A total of 840 piglets were allocated to three dietary treatments consisting of a control group (CG), an alfalfa meal group (AG), and a commodity concentrated fiber group (OG) in a 30-day feeding trial. Gut mucosa and feces samples were used to determine bacterial community diversity by 16S rRNA gene amplicon sequencing. Fiber treatment had a positive effect on growth performance and metabolism of SCFAs in piglets, in particular, compared with CG, the diarrhea rate was significantly decreased, and the content of propionic acid (PA) in the cecum was markedly increased in AG. The Shannon indices of the jejunum microbiota in AG were higher than CG. At the genus level, compared to CG, in the duodenum, the relative abundance of Paenibacillus in AG and OG was higher; in the jejunum, the relative abundances of Bacillus, Oceanobacillus, Paenibacillus, Lactococcus, Enterococcus, and Exiguobacterium were higher, whereas the relative abundance of Mycoplasma was lower in AG; in the cecum, there was also lower relative abundance of Helicobacter in AG and OG, and furthermore, the relative abundance of Faecalibacterium in OG was higher than in CG and AG. Spearman correlation analysis showed that Pseudobutyrivibrio was positively correlated with acetic acid, PA, and butyric acid (BA), while Bacteroides and Anaerotruncus were negatively correlated with PA and BA. In addition, microbiota analyses among different intestine segments showed distinct differences in microbiota between the proximal and distal intestines. Bacteria in the proximal segments were mainly Firmicutes, while bacteria in the distal segments were mainly Bacteroidetes and Firmicutes. Overall, these findings suggested that DF treatment could reduce the diarrhea rate of piglets and had beneficial effects on gut health, which might be attributed to the alteration in gut microbiota induced by DF and the interaction of the gut microbiota with SCFAs.

Differences in the Gut Microbiota Establishment and Metabolome Characteristics Between Low- and Normal-Birth-Weight Piglets During Early-Life

Low-birth-weight (LBW) piglets are at a high-risk for postnatal growth failure, mortality, and metabolic disorders later in life. Early-life microbial exposure is a potentially effective intervention strategy for modulating the health and metabolism of the host. Yet, it has not been well elucidated whether the gut microbiota development in LBW piglets is different from their normal littermates and its possible association with metabolite profiles. In the current study, 16S rRNA gene sequencing and metabolomics was used to investigate differences in the fecal microbiota and metabolites between LBW and normal piglets during early-life, including day 3 (D3), 7 (D7), 14 (D14), 21 (D21, before weaning), and 35 (D35, after birth). Compared to their normal littermates, LBW piglets harbored low proportions of Faecalibacterium on D3, Flavonifractor on D7, Lactobacillus, Streptococcus, and Prevotella on D21, as well as Howardella on D21 and D35. However, the abundance of Campylobacter on D7 and D21, Prevotella on D14 and D35, Oscillibacter and Moryella on D14 and D21, and Bacteroides on D21 was significantly higher in LBW piglets when compared with normal piglets. The results of the metabolomics analysis suggested that LBW significantly affected fecal metabolites involved in fatty acid metabolism (e.g., linoleic acid, α-linolenic acid, and arachidonic acid), amino acid metabolism (e.g., valine, phenylalanine, and glutamic acid), as well as bile acid biosynthesis (e.g., glycocholic acid, 25-hydroxycholesterol, and chenodeoxycholic acid). Spearman correlation analysis revealed a significant negative association between Campylobacter and N1-acetylspermine on D7, Moryella and linoleic acid on D14, Prevotella and chenodeoxycholic acid on D21, and Howardella and phenylalanine on D35, respectively. Collectively, LBW piglets have a different gut bacterial community structure when compared with normal-birth-weight (NBW) piglets during early-life, especially from 7 to 21 days of age. Also, a distinctive metabolic status in LBW piglets might be partly associated with the altered intestinal microbiota. These findings may further elucidate the factors potentially associated with the impaired growth and development of LBW piglets and facilitate the development of nutritional interventions.

Chronic kidney disease, uremic milieu, and its effects on gut bacterial microbiota dysbiosis

Several lines of evidence suggest that gut bacterial microbiota is altered in patients with chronic kidney disease (CKD), though the mechanism of which this dysbiosis takes place is not well understood. Recent studies delineated changes in gut microbiota in both CKD patients and experimental animal models using microarray chips. We present 16S ribosomal RNA gene sequencing of both stool pellets and small bowel contents of C57BL/6J mice that underwent a remnant kidney model and establish that changes in microbiota take place in the early gastrointestinal tract. Increased intestinal urea concentration has been hypothesized as a leading contributor to dysbiotic changes in CKD. We show that urea transporters (UT)-A and UT-B mRNA are both expressed throughout the whole gastrointestinal tract. The noted increase in intestinal urea concentration appears to be independent of UTs' expression. Urea supplementation in drinking water resulted in alteration in bacterial gut microbiota that is quite different than that seen in CKD. This indicates that increased intestinal urea concentration might not fully explain the CKD- associated dysbiosis.

Dietary L-Tryptophan Modulates the Structural and Functional Composition of the Intestinal Microbiome in Weaned Piglets

Background: Intestinal microbiota plays an important role in regulating metabolism, physiology, and immune response of the host. L-Tryptophan (Trp) are metabolized by several genera of bacteria. It remains largely unknown whether Trp can regulate the composition and diversity of the intestinal microbiota and contribute to intestinal homeostasis.

Methods: A total of 126 weaning piglets were fed a corn- and soybean meal-based diet supplemented with 0, 0.2, or 0.4% Trp for 4 weeks. The intestinal microbiota was measured by using bacterial 16S rRNA gene-based high-throughput sequencing methods. Metabolites of Trp and short-chain fatty acids (SCFAs) in the hindgut were determined by high-performance liquid chromatography and gas chromatography, respectively. The mRNA levels for aromatic hydrocarbon receptor (AhR), tumor necrotic factor-α (TNF-α), interleukin-8 (IL-8), and protein abundances of tight junction proteins were determined.

Results: Compared with the control group, Trp supplementation enhanced piglet growth performance and markedly altered the intestinal microbial composition as evidenced by enhanced alpha and beta diversity in the microbiome (P < 0.05). The abundances of Prevotella, Roseburia, and Succinivibrio genera were enriched, but those of Clostridium sensu stricto and Clostridium XI, opportunistic pathogens, were decreased with dietary Trp supplementation. Analysis of metabolic pathways indicated enhanced indole alkaloid biosynthesis and Trp metabolism, which was validated by elevated concentrations of 3-indoleacetic acid and indole in the intestinal contents of Trp-supplemented piglets (P < 0.05). These changes in Trp metabolites were correlated with activation of AhR and cytochrome p4501 A1 (CYP1A1) in cecum and colonic tissues, and with a decrease in the intestinal mucosal IL-8 mRNA level. Moreover, the protein abundances for zonula occluden (ZO)-1 and occludin were upregulated by Trp supplementation in colonic tissues.

Conclusion: Dietary Trp supplementation altered intestinal microbial composition and diversity, improved intestinal mucosal barrier function, activated AhR signaling, and downregulated expression of inflammatory cytokines in the large intestine of weaned piglets. These results indicate a crosstalk between dietary Trp and intestine in nutrition, microbial metabolism, and mucosal immunity.

Gut microbial diversity in two insectivorous bats: Insights into the effect of different sampling sources

The gut microbiota is now known as a key factor in mammalian physiology and health. Our understanding of the gut microbial communities and their effects on ecology and evolution of their hosts is extremely limited in bats which represent the second largest mammalian order. In the current study, gut microbiota of three sampling sources (small intestine, large intestine, and feces) were characterized in two sympatric and insectivorous bats (Rhinolophus sinicus and Myotis altarium) by high‐throughput sequencing of the V3‐V4 region of the 16S rRNA gene. Combining with published studies, this work reveals that Gammaproteobacteria may be a dominant class in the whole Chiroptera and Fusobacteria is less observed in bats although it has been proven to be dominant in other mammals. Our results reveal that the sampling source influences alpha diversity of the microbial community in both studied species although no significant variations of beta diversity were observed, which support that fecal samples cannot be used as a proxy of the microbiota in other gut regions in wild animals.

Ileum terminal antibiotic infusion affects jejunal and colonic specific microbial population and immune status in growing pigs

Background

Compared with oral antibiotics (primarily disrupt foregut microbiota), the present study used antibiotics with ileum terminal infusion to disrupt the hindgut microbiota, and investigated the changes in specific bacterial composition and immune indexes in the jejunum and colon, and serum of growing pigs. Twelve barrows (45 d of age, 12.08 ± 0.28 kg) fitted with a T-cannula at the terminal ileum, were randomly assigned to two groups and infused either saline without antibiotics (Control) or with antibiotics (Antibiotic) at the terminal ileum. After 25 d experiment, all pigs were euthanized for analyzing bacterial composition and immune status.

Results

Ileum terminal antibiotic infusion (ITAI) altered dominant bacteria counts, with a decrease in Bifidobacterium, Clostridium cluster IV and Clostridium cluster IV in the colon (P < 0.05), and an increase in Escherichia coli in the jejunum (P < 0.05). ITAI decreased (P < 0.05) short-chain fatty acids concentrations in the colon. ITAI decreased interleukin-8 (IL-8), IL-10 and secretory immunoglobulin A (sIgA) concentrations, and down-regulated IL-10, Mucin-1 (MUC1), Mucin-2 (MUC2) and zonula occludens-1 (ZO-1) mRNA expression in the colonic mucosa (P < 0.05). In the jejunal mucosa, ITAI decreased interferon-γ (IFN-γ), tumor necrosis factor-α (TNF-α), sIgA and IgG levels together with down-regulation of IFN-γ, TNF-α, MUC2 and ZO-1 mRNA expression (P < 0.05). Furthermore, ITAI decreased IL-10, INF-γ, TNF-α, IgA and IgG concentrations in serum (P < 0.05). Correlation analysis revealed that the change in intestinal microbiota was correlated with alterations of Ig and cytokines.

Conclusions

ITAI affected jejunal and colonic specific bacteria counts, and altered some immune markers levels in the jejunal and colonic mucosa and serum. These findings implicate the potential contribution of hindgut bacteria to immune response in the intestinal mucosa and serum of growing pigs.

Electronic supplementary material

The online version of this article (10.1186/s40104-018-0265-x) contains supplementary material, which is available to authorized users.

Comparative Analysis of Ileal and Cecal Microbiota in Aged Rats

Background

Gut microbiota contributes to intestinal and immune homeostasis through host-microbiota interactions. Distribution of the gut microbiota differs according to the location in the gastrointestinal tract. Although the microbiota properties change with age, evidence for the regional difference of gut microbiota has been restricted to the young. The aim of this study is to compare the gut microbiota between terminal ileum and cecum of old rats.

Methods

We analyzed gut microbiome of luminal contents from ileum and cecum of 74-week-old and 2-year-old rats (corresponding to 60-year and 80-year-old of human age) by metagenome sequencing of 16S rRNA.

Results

Inter-individual variation (beta diversity) of microbiota was higher in ileum than in cecum. Conversely, alpha diversity of microbiota composition was higher in cecum than in ileum. Lactobacillaceae were more abundant in ileum compared to cecum while Ruminococcaceae and Lachnospiraceae were more enriched in cecum. The proportions of Deltaproteobacteria were increased in cecal microbiota of 2-year-old rats compared to 74-week-old rats.

Conclusions

Major regional distinctions of microbiota between ileum and cecum of old rats appear consistent with those of young rats. Age-related alterations of gut microbiota in old rats seem to occur in minor compositions.

Marked Response in Microbial Community and Metabolism in the Ileum and Cecum of Suckling Piglets After Early Antibiotics Exposure

In modern swine husbandry systems, antibiotics have been used as growth promoters for piglets during suckling or weaning period. However, while early colonization of intestinal microbiota has been regarded crucial for the host’s later life performance and well-being, little is known about the impact of antibiotics on intestinal microbiota in suckling piglets. The present study aimed to investigate the effects of early antibiotics exposure on gut microbiota and microbial metabolism of suckling piglets. Sixteen litters of suckling piglets were fed a creep feed diet with (Antibiotic) or without (Control) antibiotics from postnatal days 7–23 (n = 8). The ileal and cecal digesta were obtained for microbial composition and microbial metabolites analysis. The results showed that the antibiotics significantly altered the bacterial community composition by decreasing (P < 0.05) the diversity and richness in the ileum. The antibiotics significantly reduced the abundance of Lactobacillus in both the ileum and cecum, increased the abundance of Streptococcus, unclassified Enterococcaceae, unclassified Fusobacteriales, and Corynebacterium in the ileum, and the abundance of unclassified Ruminococcaceae and unclassified Erysipelotrichaceae in the cecum. The antibiotics decreased (P < 0.05) ileal lactate concentration and cecal concentration of total short-chain fatty acids (SCFAs). But the antibiotics enhanced protein fermentation (P < 0.05) in the ileum and cecum, as ileal concentrations of putrescine and cadaverine, and cecal concentrations of isobutyrate, isovalerate, putrescine, cadaverine, spermine, and spermidine were significantly increased (P < 0.05). These results indicated that early antibiotics exposure significantly altered the microbial composition of suckling piglets toward a vulnerable and unhealthy gut environment. The findings provide a new insight on the antibiotics impact on neonates and may provide new framework for designing alternatives to the antibiotics toward a healthy practice for suckling piglets.

Time-course responses of ileal and fecal microbiota and metabolite profiles to antibiotics in cannulated pigs

We investigated the time-course effects of therapeutic antibiotics on intestinal microbial composition and metabolism in an ileal-cannulated pig model. Sixteen ileal-cannulated piglets (12 ± 0.5 kg) were assigned to two groups (n = 8) and fed standard diets with or without antibiotics. At 4 days before, and at days 2, 7, and 13 after antibiotic administration, ileal and fecal samples were collected for analysis of microbiota composition via 16S rRNA MiSeq sequencing and metabolites (short-chain fatty acids, biogenic amines, and indole). It was found that Lactobacillus and Bifidobacterium had decreased by an average 2.68-fold and 508-fold in ileum on days 2-13, and by an average 45.08-fold and 71.50-fold in feces on days 7-13 (P < 0.05). Escherichia/Shigella had increased by an average 265-fold in ileum on days 2-13, and by an average 36.70-fold in feces on days 7-13 (P < 0.05). Acetate concentration had decreased in ileum by an average 2.88-fold on days 2-13, and by 1.83-fold in feces on day 7 (P < 0.05). Cadaverine concentration had increased by an average 7.03-fold in ileum on days 2-13, and by an average 9.96-fold in feces on days 7-13 (P < 0.05), and fecal indole concentration had increased by an average 2.51-fold on days 7-13 (P < 0.05). Correlation analysis between significant microbes and metabolites indicated that the antibiotic-induced microbiota shift appeared to result in the changes of intestinal metabolism. In conclusion, antibiotic administration led to dynamic changes in microbial communities and metabolism in ileum and feces, with ileal microbiota being more prone to shift than fecal microbiota.

Shifting trends in bacteriology and antimicrobial resistance among gastrointestinal fistula patients in China: an eight-year review in a tertiary-care hospital

BACKGROUND

The purpose of this study was to determine the shifting trends in bacteriology and antimicrobial resistance of infectious specimens isolated from gastrointestinal (GI) fistula patients over eight years in China.

METHODS

We retrospectively reviewed the microbial records of intra-abdominal specimens at a teaching hospital from 2008 to 2015. Study period was divided into the first half (2008-2011) and the second half (2012-2015). All isolates underwent antibiotic susceptibility testing by the micro dilution method.

RESULTS

A total of 874 intra-abdominal isolates were consecutively collected from 502 GI fistula patients (mean age, 46.5 years, 71.1% male) during the study period. Patients in the second study period (2012-2015) were older (>65 years) and more likely to have experienced cancer. Over the entire study period, most infections were caused by E. coli (24.2%) and K. pneumonia (14.1%). There was a significant decrease in the proportion E. coli isolates that were extended- spectrum beta-lactamase (ESBL)-positive (P = 0.026). The proportion of E. coli resistant to imipenem increased from 14.3% in 2008-2011 to 25.9% in 2012-2015 (P = 0.037). Imipenem resistance prevalence was higher in ESBL-negative bacteria than ESBL-positive bacteria for both E. coli and K. pneumonia (P < 0.001). In Enterococcus, significant increase in resistance to ampicillin (P = 0.01) and moxifloxacin (P = 0.02) over time were observed. In Staphylococcus and fungi, rates of antibiotic resistance did not significantly change over the study period.

CONCLUSIONS

Gram-negative bacteria predominated as causative agents of intra-abdominal infections in GI fistula patients, and there was an increase in levels of resistance to certain antibiotics, particularly carbapenems. Infection control and source control are important tools available to surgeons to prevent the emergence of antibiotic-resistant pathogens.

Segment-specific responses of intestinal epithelium transcriptome to in-feed antibiotics in pigs

Despite widespread use of antibiotics for treatment of human diseases and promotion of growth of agricultural animals, our understanding of their effects on the host is still very limited. We used a model in which pigs were fed with or without a cocktail of antibiotics and found, based on the denaturing gradient gel electrophoresis (DGGE) patterns, that the fecal bacteria from the treatment and control animals were distinct. Furthermore, the total bacterial population in the feces tended to be decreased by the antibiotic treatment (P = 0.07), and the counts of Lactobacillus and Clostridium XIVa were significantly reduced (P < 0.05). To explore the effects of antibiotics on host intestinal epithelium, we assessed gene expression profiles of the jejunum and ileum and their response to antibiotic administration. The results indicate that in-feed antibiotics increased expression of genes involved in immune functions in both the jejunum and ileum, some of which were clustered in the coexpression network. Gene ontology terms of metabolic processes were altered predominantly in the jejunum but not in the ileum. Notably, antibiotics diminished intestinal segment-specific transcriptional changes, especially for genes associated with metabolic functions. This study reveals segment-specific responses of host intestinal epithelium to in-feed antibiotics, which can be a valuable resource for deciphering antibiotic-microbiota-host interactions.