Fecal Composition Research Articles

Diet Composition and Using Probiotics or Symbiotics Can Modify the Urinary and Faecal Nitrogen Ratio of Broiler Chicken's Excreta and Also the Dynamics of In Vitro Ammonia Emission.

The objective of this research was to determine whether diet composition, or adding probiotic or symbiotic feed additives to broiler diets can modify the N composition of the excreta and the dynamics of ammonia volatilization from the manure. A total of 574 one-day-old Ross 308 broiler chickens were fed four different diets. The treatments included a corn and soybean meal-based control diets (C), wheat-based and wheat bran containing diets (W), a multi-strain probiotic treatment (Broilact®; Br), and a symbiotic additive containing Bacillus subtilis, inulin, and Saccharomices cerevisiae (Sy). Feeding the wheat-based diet significantly improved the weight gain and FCR of chickens. Treatment W also significantly increased the dry matter content of the excreta compared with the probiotic and symbiotic treatments. Both Br and Sy tended to decrease the amount of excreted uric acid, which is the main substrate of ammonia. Treatment Sy reduced the urinary N ratio of the excreta in comparison with treatment W. The symbiotic additive resulted in significantly higher ammonia emission in the first two hours. On the other hand, the dynamics of the emission was slow at the beginning and increased steeply after 15 h when the wheat-based diets were fed. Based on our results, the wheat-based diets, containing soluble arabinoxylans, and the symbiotic treatments of broiler diets have an impact on the urinary and faecal nitrogen composition of the excreta, and also on the dynamics of ammonia release from the manure.

Obstructive sleep apnea is related to alterations in fecal microbiome and impaired intestinal barrier function

Obstructive Sleep Apnea (OSA) is related to repeated upper airway collapse, intermittent hypoxia, and intestinal barrier dysfunction. The resulting damage to the intestinal barrier may affect or be affected by the intestinal microbiota. A prospective case–control was used, including 48 subjects from Sleep Medicine Center of Nanfang Hospital. Sleep apnea was diagnosed by overnight polysomnography. Fecal samples and blood samples were collected from subjects to detect fecal microbiome composition (by 16S rDNA gene amplification and sequencing) and intestinal barrier biomarkers—intestinal fatty acid-binding protein (I-FABP) and D-lactic acid (D-LA) (by ELISA and colorimetry, respectively). Plasma D-LA and I-FABP were significantly elevated in patients with OSA. The severity of OSA was related to differences in the structure and composition of the fecal microbiome. Enriched Fusobacterium, Megamonas, Lachnospiraceae_UCG_006, and reduced Anaerostipes was found in patients with severe OSA. Enriched Ruminococcus_2, Lachnoclostridium, Lachnospiraceae_UCG_006, and Alloprevotella was found in patients with high intestinal barrier biomarkers. Lachnoclostridium and Lachnospiraceae_UCG_006 were the common dominant bacteria of OSA and intestinal barrier damage. Fusobacterium and Peptoclostridium was independently associated with apnea–hypopnea index (AHI). The dominant genera of severe OSA were also related to glucose, lipid, neutrophils, monocytes and BMI. Network analysis identified links between the fecal microbiome, intestinal barrier biomarkers, and AHI. The study confirms that changes in the intestinal microbiota are associated with intestinal barrier biomarkers among patients in OSA. These changes may play a pathophysiological role in the systemic inflammation and metabolic comorbidities associated with OSA, leading to multi-organ morbidity of OSA.

Raw potato starch alters the microbiome, colon and cecal gene expression, and resistance to Citrobacter rodentium infection in mice fed a Western diet.

Resistant starches (RS) are fermented in the cecum and colon to produce short-chain fatty acids and other microbial metabolites that can alter host physiology and the composition of the microbiome. We previously showed that mice fed a Total Western Diet (TWD) based on NHANES data that mimics the composition of a typical American diet, containing resistant potato starch (RPS), produced concentration dependent changes to the cecal short-chain fatty acids, the microbiome composition as well as gene expression changes in the cecum and colon that were most prevalent in mice fed the 10% RPS diet. We were then interested in whether feeding TWD/RPS would alter the resistance to bacterial-induced colitis caused by Citrobacter rodentium (Cr), a mouse pathogen that shares 66.7% of encoded genes with Enteropathogenic Escherichia coli. Mice were fed the TWD for 6 weeks followed by a 3-weeks on the RPS diets before infecting with Cr. Fecal Cr excretion was monitored over time and fecal samples were collected for 16S sequencing. Mice were euthanized on day 12 post-infection and cecal contents collected for 16S sequencing. Cecum and colon tissues were obtained for gene expression analysis, histology and to determine the level of mucosa-associated Cr. Feeding RPS increased the percentage of mice productively infected by Cr and fecal Cr excretion on day 4 post-infection. Mice fed the TWD/10% RPS diet also had greater colonization of colonic tissue at day 12 post-infection and colonic pathology. Both diet and infection altered the fecal and cecal microbiome composition with increased levels of RPS resulting in decreased α-diversity that was partially reversed by Cr infection. RNASeq analysis identified several mechanistic pathways that could be associated with the increased colonization of Cr-infected mice fed 10% RPS. In the distal colon we found a decrease in enrichment for genes associated with T cells, B cells, genes associated with the synthesis of DHA-derived SPMs and VA metabolism/retinoic acid signaling. We also found an increase in the expression of the potentially immunosuppressive gene, Ido1. These results suggest that high-level consumption of RPS in the context of a typical American diet, may alter susceptibility to gastrointestinal bacterial infections.

Akkermansia deficiency and mucin depletion are implicated in intestinal barrier dysfunction as earlier event in the development of inflammation in interleukin-10-deficient mice.

Dysbiosis and mucin depletion are related with intestinal barrier dysfunction and seems to be an early pathophysiological event in inflammatory bowel disease (IBD). The objective of this work is to study these parameters in the natural history of colitis in IL-10 deficient mice (IL-10-/-). Wild type (WT) and IL-10-/-. mice were followed until sacrifice at 3, 5, 10, 20, 57, and 70 weeks. Body weight, colonic weight/length ratio and in vivo intestinal permeability were registered. Expression of inflammatory and adhesion molecules in the colon was explored by qPCR as Mucin-2 (MUC-2) and molecules involved in goblet cell maturation Interleukin-18 (IL-18) and WAP Four-Disulfide Core Domain 2 (WFDC2), the endoplasmic reticulum stress markers X-box-binding protein (Xbp-1) and Reticulon-4B (RTN-4B). Bacterial composition in feces and colonic mucosa was determined by massive sequencing of the V3-V4 regions of 16S rDNA gene. IL-10-/- mice showed histological inflammation at weeks 20 and 57, but most notably the intestinal permeability was significantly higher from week 10. Concordantly, the number of goblet cells and expression of MUC-2, IL-18, WFDC2 and Xbp-1 were significantly lower in KO from week 10. Nevertheless, no significant differences were found in the mRNA expression of MUC-2 or Xbp-1 between both groups-derived colon organoids. Significant bacterial differences began at week 5, being the Akkermansia deficiency in KO the most relevant result. Gut microbiota alterations and mucin depletion are associated with early intestinal barrier dysfunction and precede overt gut inflammation in this animal model of IBD.

Maternal diet associated with infants' intestinal microbiota mediated by predominant long-chain fatty acid in breast milk.

Long-chain fatty acids in breast milk are affected by the mother's diet and play an important role in the growth, development, and immune construction of infants. This study aims to explore the correlation between maternal diet, breast milk fatty acids (FAs), and the infant intestinal flora. We enrolled 56 paired mothers and their infants; both breast milk samples and infants' fecal samples were collected to determine the long-chain FA content of breast milk by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS), and metagenomic technology was applied to determine the microbial composition of infant feces. The maternal diet was also investigated using a 24-h dietary recall. The results indicated that the fat contribution rates of edible oils in the maternal diet are significantly positively correlated with the contents of certain long-chain fatty acids (C16:0, C18:1, C16:1, and C22:4) in breast milk, which mainly regulate the abundance of Lacticaseibacillus rhamnosus, Lacticaseibacillus fermentum, and Lacticaseibacillus paracasei in the infant gut. Through KEGG pathway analysis, our data revealed that the long-chain FAs in different groups of breast milk were significantly correlated with the pathways of biotin metabolism, glycerolipid metabolism, and starch and sucrose metabolism. The results of this study suggest a pathway in which the diets of lactating mothers may affect the composition of the infant intestinal microbiota by influencing breast milk FAs and then further regulating infant health.

Weikangling capsules combined with omeprazole ameliorates ethanol-induced chronic gastritis by regulating gut microbiota and EGF-EGFR-ERK pathway

AimsWeikangling capsules (WKLCs) have been widely used in the treatment of chronic gastritis. Whether used alone or combined with omeprazole (OME), it shows a significant effect. However, the mechanisms haven't been established. The study aimed to explore the mechanisms of WKLCs and its combination with OME on chronic gastritis. Main methodsThe components of WKLCs and EA (the ethyl acetate extraction extracted from WKLCs) fraction were analyzed. Then chronic gastritis model rats were induced by 56 % ethanol and treated with OME, low dose of WKLCs (WKL), high dose of WKLCs (WKH), WKLCs combined with OME (WO), and EA fraction (EA) to evaluate the mechanisms of WKLCs, drug combination and EA fraction. Key findingsA total of 22 components of WKLCs were quantified, among them 18 were enriched in EA fraction. WKLCs alleviated the morphology and inflammation of gastric mucosa and downregulated the levels of inflammatory factors (IL-1β, TNF-α, IL-6) and epidermal growth factor (EGF) in serum by inhibiting the EGF-EGFR-ERK pathway, regulating gut microbiota composition and SCFAs contents in feces. WKLCs plus OME was better than OME. EA fraction improved digestive function by increasing pepsin activity and decreasing gastrointestinal hormones (GAS and VIP) compared with WKLCs. SignificanceThis study elucidated that the effect of WKLCs and its combination with OME in the treatment of chronic gastritis was attributed to regulating the composition of the gut microbiota and inhibiting the EGF-EGFR-ERK pathway. The EA fraction is an inseparable effective substance of WKLCs. This study provides scientific evidence for clinical application.

Predicting fecal composition, intake, and nutrient digestibility in beef cattle consuming high forage diets using near infrared spectroscopy.

The objective of this study was to develop near infrared spectroscopy (NIRS) calibrations to predict fecal nutrient composition, intake, and diet digestibility from beef cattle fed high forage diets. Heifers were fed 12 different forage-based diets (>95% forage dry matter basis) in 3 total collection digestibility studies, resulting in individual fecal samples and related spectra (n = 135), corresponding nutrient intake, and apparent total tract digestibility (aTTD) data. Fecal samples were also collected from steers grazing two annual and two perennial forage mixtures over two growing seasons. Samples (n = 13/paddock) were composited by paddock resulting in 30 samples from year 1, and 24 from year 2. The grazing fecal spectra (n = 54) were added to the existing fecal composition spectral library. Dried and ground fecal samples were scanned using a FOSS DS2500 scanning monochromator (FOSS, Eden Prairie, MN). Spectra were mathematically treated for detrend and scatter correction and modified partial least squares (MPLS) regression was performed. The coefficient of determination for cross validation (R2cv) and standard error of cross validation (SECV) were used to evaluate the quality of calibrations. Prediction equations were developed for fecal composition [organic matter (OM), nitrogen (N), amylase-treated ash-corrected neutral detergent fiber (aNDFom), acid detergent fiber (ADF), acid detergent lignin (ADL), undigestible NDF after 240 h of in vitro incubation (uNDF), calcium (Ca), and phosphorus (P)], digestibility [DM, OM, aNDFom, N], and intake [DM, OM, aNDFom, N, uNDF]. The calibrations for fecal OM, N, aNDFom, ADF, ADL, uNDF, Ca, P resulted in R2cv between 0.86 and 0.97 and SECV of 1.88, 0.07, 1.70, 1.10, 0.61, 2.00, 0.18, and 0.06, respectively. Equations predicting intake of DM, OM, N, aNDFom, ADL, and uNDF resulted in R2cv values between 0.59 and 0.91, SECV values of 1.12, 1.10, 0.02, 0.69, 0.06, 0.24 kg·d-1, respectively, and SECV values between 0.00 and 0.16 when expressed as % body weight (BW). Digestibility calibrations for DM, OM, aNDFom, and N resulted in R2cv ranging from 0.65 to 0.74 and SECV values from 2.20 to 2.82. We confirm the potential of NIRS to predict fecal chemical composition, digestibility, and intake of cattle fed high forage diets. Future steps include validation of the intake calibration equations for grazing cattle using forage internal marker and modelling energetics of grazing growth performance.

Plant-based polyphenol rich protein supplementation attenuated skeletal muscle loss and lowered the LDL level via gut microbiota remodeling in Taiwan's community-dwelling elderly.

Sarcopenia, characterized by muscle loss, negatively affects the elderly's physical activity and survival. Enhancing protein and polyphenol intake, possibly through the supplementation of fermented black soybean koji product (BSKP), may alleviate sarcopenia by addressing anabolic deficiencies and gut microbiota dysbiosis because of high contents of polyphenols and protein in BSKP. This study aimed to examine the effects of long-term supplementation with BSKP on mitigating sarcopenia in the elderly and the underlying mechanisms. BSKP was given to 46 participants over 65 years old with early sarcopenia daily for 10 weeks. The participants' physical condition, serum biochemistry, inflammatory cytokines, antioxidant activities, microbiota composition, and metabolites in feces were evaluated both before and after the intervention period. BSKP supplementation significantly increased the appendicular skeletal muscle mass index and decreased the low-density lipoprotein level. BSKP did not significantly alter the levels of inflammatory factors, but significantly increased the activity of antioxidant enzymes. BSKP changed the beta diversity of gut microbiota and enhanced the relative abundance of Ruminococcaceae_UCG_013, Lactobacillus_murinus, Algibacter, Bacillus, Gordonibacter, Porphyromonas, and Prevotella_6. Moreover, BSKP decreased the abundance of Akkermansia and increased the fecal levels of butyric acid. Positive correlations were observed between the relative abundance of BSKP-enriched bacteria and the levels of serum antioxidant enzymes and fecal short chain fatty acids (SCFAs), and Gordonibacter correlated negatively with serum low-density lipoprotein. In summary, BSKP attenuated age-related sarcopenia by inducing antioxidant enzymes and SCFAs via gut microbiota regulation. Therefore, BSKP holds potential as a high-quality nutrient source for Taiwan's elderly, especially in conditions such as sarcopenia.

Gut indigenous Ruminococcus gnavus alleviates constipation and stress-related behaviors in mice with loperamide-induced constipation.

Refractory constipation is the most severe form of constipation, and its etiology remains unknown. The symptoms of constipation occur repeatedly, which brings great pain to the patient's body and psychology. Accumulating studies suggest that constipation patients present a significant dysbiosis of the gut microbiota compared with healthy individuals. In this study, we analyzed the gut microbiota composition of fresh feces and accumulated feces (old feces) of patients with refractory constipation and found that there was a significant difference between them. Through a mouse model of loperamide-induced constipation, it was proved that the old feces of patients with refractory constipation could aggravate the constipation symptoms in mice, while the fresh feces could alleviate the symptoms, which is consistent with the effect of feces from healthy volunteers in a mouse model of loperamide-induced constipation. We identified an indigenous strain Ruminococcus gnavus (R. gnavus), which is highly enriched in the fresh feces of patients with refractory constipation, and found that oral administration of R. gnavus could effectively improve the constipation symptoms in mice with constipation induced by loperamide and fecal bacteria transplanted from patients with constipation and significantly improve the stress-related behaviors of mice. This result may be related to the regulation of intestinal muc2, c-kit, sert and other gene expression by R. gnavus and the control of somatostatin (SS) and motilin (MTL) production. Our results suggest that gut microbe intervention with indigenous strains such as R. gnavus is a potential and promising alternative for the treatment of constipation, especially for refractory constipation.

Host genotype affects endotoxin release in excreta of broilers at slaughter age.

Host genotype, early post-hatch feeding, and pre- and probiotics are factors known to modulate the gut microbiome. However, there is a knowledge gap on the effect of both chicken genotype and these dietary strategies and their interplay on fecal microbiome composition and diversity, which, in turn, can affect the release of endotoxins in the excreta of broilers. Endotoxins are a major concern as they can be harmful to both animal and human health. The main goal of the current study was to investigate whether it was possible to modulate the fecal microbiome, thereby reducing endotoxin concentrations in the excreta of broiler chickens. An experiment was carried out with a 2 × 2 × 2 factorial arrangement including the following three factors: 1) genetic strain (fast-growing Ross 308 vs. slower growing Hubbard JA757); 2) no vs. combined use of probiotics and prebiotics in the diet and drinking water; and 3) early feeding at the hatchery vs. non-early feeding. A total of 624 Ross 308 and 624 Hubbard JA757 day-old male broiler chickens were included until d 37 and d 51 of age, respectively. Broilers (N = 26 chicks/pen) were housed in a total of 48 pens, and there were six replicate pens/treatment groups. Pooled cloacal swabs (N = 10 chickens/pen) for microbiome and endotoxin analyses were collected at a target body weight (BW) of 200g, 1kg, and 2.5kg. Endotoxin concentration significantly increased with age (p = 0.01). At a target BW of 2.5kg, Ross 308 chickens produced a considerably higher amount of endotoxins (Δ = 552.5EU/mL) than the Hubbard JA757 chickens (p < 0.01). A significant difference in the Shannon index was observed for the interaction between the use of prebiotics and probiotics, and host genotype (p = 0.02), where Ross 308 chickens with pre-/probiotics had lower diversity than Hubbard JA757 chickens with pre-/probiotics. Early feeding did not affect both the fecal microbiome and endotoxin release. Overall, the results suggest that the chicken genetic strain may be an important factor to take into account regarding fecal endotoxin release, although this needs to be further investigated under commercial conditions.

The fecal microbiomes analysis of Marabou storks (Leptoptilos crumenifer) reveals their acclimatization to the feeding environment in the Kampala urban areas, Uganda.

The Marabou stork (Leptoptilos crumenifer) is a typical scavenging bird and adapted to the Savannah environment, where they show a carnivorous feeding style. However, Marabou stork recently penetrated into the city areas and acclimatized to the urban environment, where they modified their feeding habits to an omnivorous type toward more carbohydrate. To reveal their adaptation to the variable feeding customs, this study compared the gut microbiomes and chemical compositions of feces of Marabou storks inhabiting two different locations in peri urban Kampala: one is a slaughter house floc that predicted their original carnivorous feeding, and the other is a landfill floc that adapted more to the omnivorous feeding. 16S rRNA gene sequencing analysis revealed more diverse gut microbiome, more enriched Lactobacilli, and less abundant Peptostreptococci in the landfill flock comparing to the slaughter house flock. Isolation work and predicted metagenome analysis confirmed more diverse Lactobacilli and more enriched functions for carbohydrate metabolism in the landfill flock. In addition, chemical composition of feces revealed higher ammonia in the former, which is consisting with higher Peptostreptococci and their practice of carnivorous feeding. These results highlighted their adaptation to the variable feeding environment, which presumably protects their health and ensure survival of species.

Lacticaseibacillus casei decrease long-chain fatty acids and most substances in an experimental model of intestinal mucositis.

To evaluate the long-chain fatty acid and major compounds levels in the feces after prophylactic oral use of Lacticaseibacillus casei in an experimental model of intestinal mucositis. Fifteen Swiss mice were randomly divided into three groups (n=5/group): The negative or positive control groups (n = 5) received saline orally for 18 days and an the intraperitoneal (i.p.) of saline or 5 Fluorouracil (450 mg/kg) in 15th day, respectability. L. casei group received oral concentration of L. casei (1x109 CFU/mL) for 18 days, the i.p. injection of 5-fluorouracil (450 mg/kg) in 15th days. Tissue samples from colon and each small intestine segment were collected for histopathological analysis. Stool samples were collected. Fecal composition of long-chain fatty acids and sterols were analysed by gas chromatography-mass spectrometry on the 15th and the 18th day. The mucosa layer of all small intestine segments of animals from L. casei showed well preserved epithelium and glands, without necrosis signs, but Goblet cells number decreased. Several long-chain fatty acids and sterols have been identified before and after in the groups. L. casei administration after 5-FU treatment reduced concentrations of linoleic acid (18:2) (p < 0.001) and oleic acid (18:1) (p < 0.001) in feces. L. casei prevented the mucosal damage associated with 5-FU-induced intestinal mucositis reduced long-chain fatty acid levels in the feces.

Results of a Clinical Trial Showing Changes to the Faecal Microbiome in Racing Thoroughbreds after Feeding a Nutritional Supplement

Next-generation sequencing (NGS) has been used to evaluate the effect of various interventions on the equine microbiome. The aim of this randomised blinded clinical trial was to determine if a prebiotic nutritional supplement would result in a change from baseline in the faecal microbiome composition of racing Thoroughbred horses in training being fed a high concentrate/grain-based diet to be more similar to that found in forage fed/pasture grazed horses. Thirty-two horses on one training yard were randomised to either receive the supplement or not. Faecal samples were collected at baseline, 6 and 12 weeks for NGS of the 16S ribosomal subunit gene. Twenty-two horses completed the trial, met the inclusion criteria and were included in the intention to treat analysis; 20 horses were included in the per protocol analysis. The mean and median percent decreases in Bacteroidetes, increases in Firmicutes and the Firmicutes:Bacteroidetes ratio were significantly greater than zero for the treated horses only. Supplemented horses (8/10) were more likely than control horses (2/10) to show an increase in Firmicutes of a ≥9% with ≥24% increase in Clostridia, ≥5% decrease in Bacteroidetes, ≥16% increase in the F:B ratio and ≥2% increase in Actinobacteria (RR = 4, 95% CI: 1.1-14.4, p = 0.01). This provides useful information for further investigations on long-term effects on the microbiome and on health and racing-related outcomes.

Effects of dietary supplementation with bioactive peptides derived from rapeseed protein on the growth performance, serum biochemistryand faecal micro-organism composition of weaned piglets.

The present study investigated the effects of supplementing bioactive peptides derived from rapeseed protein (rapeseed peptide, Rsp) on the growth performance, serum biochemistryand faecal micro-organism composition of weaned piglets. Sixty Duroc × Landrace × Yorkshire weaned piglets of similar weights were randomly divided into three groups. The control group (NC) was fed a basal diet, and the two treatment groups, Rsp-1 and Rsp-2, were fed a basal diet supplemented with 1% or 2% Rsp, respectively, for 28 days. Each treatment consisted of five replicates with four piglets per replicate. The results showed that Rsp treatment significantly improved the average daily gain and had a better feed-to-gain ratio (p < 0.05). The diarrhoea incidence and indices of Rsp-1 and Rsp-2 groups were significantly lower than the NC group (p < 0.05), and the effect of Rsp-2 on reducing the incidence of diarrhoea was significantly higher than that of Rsp-1 (p < 0.05). The serum albumin, serum immunoglobulin Aand catalase levels of the Rsp-1 and Rsp-2 groups were significantly better than the NC group (p < 0.05). Additionally, Rsp treatment significantly gained the relative abundance of faecal Lactobacillaceae and decreased the relative abundance of faecal Eubacterium_coprostanoligenes_group, Treponemaand Coprococcus (p < 0.05). In summary, Rsp supplementation improved the growth performance, ameliorated the diarrhoea, enhanced the immune and antioxidant functionsand changed the composition of faecal micro-organisms in piglets. These findings indicate that Rsp positively affected the health of weaned piglets.

Effect of a Diet Based on Biotransformed Sorghum on Rabbit Intestinal Morphology and Fecal Fiber Composition

Some of the goals of meat production systems are to improve feed efficiency, reduce costs, provide proper nutrition and avoid metabolic disorders. Hence, the aim of this work was to compare a rabbit diet based on untreated sorghum (T1) with a second one that included the cereal biotransformed by the co-cultivation of two basidiomycetes (T2). Their effects on the cereal, diets, and fecal structural fiber composition, as well as on rabbit intestinal morphology, were evaluated. A completely randomized design was applied, employing 24 New Zealand rabbits (21 days old). The fiber chemical composition results indicated that the sorghum treated with the co-culture had lower amounts of neutral detergent fiber (NDF), acid detergent fiber (ADF), lignin, hemicellulose and cellulose, as did rabbits fed the T2 diet. Decreases in the NDF, ADF and cellulose contents were detected in T2-nourished rabbit excrements at day 21 (p ≤ 0.05), while lignin percentages diminished at days 35 and 49 (p ≤ 0.05). These rabbits also showed longer jejunal and cecal villi (p ≤ 0.05). The results obtained suggest a positive effect on the bioavailability of structural fibers after sorghum fungal co-fermentation, as their content decreased in rabbit fecal matter without damaging the intestinal morphology.

Microbial composition of carapace, feces, and water column in captive juvenile green sea turtles with carapacial ulcers.

Green sea turtles are endangered marine reptiles. Carapacial ulcers will develop on juvenile green sea turtles during artificial rescue, seriously affecting their health and potentially leading to death. To determine the pathogens causing ulcerative carapacial disease, we performed 16S and ITS high-throughput sequencing, and microbial diversity analysis on samples from carapacial ulcers, healthy carapaces, feces, and seawater of juvenile green sea turtles. Our analysis showed that changes in microbial diversity of green sea turtle feces and seawater were not significantly associated with ulcerative carapacial disease. Psychrobacter sp. is the dominant species in the carapacial ulcers of green sea turtles. The bacterium is present in both healthy turtles and seawater where carapacial ulcers did not occur and decreasing seawater temperatures are likely responsible for the infection of juvenile green turtles with Psychrobacter sp. This is the first study on carapacial ulcers in captive juvenile green sea turtles. Our research provides theoretical guidance for the prevention and control of carapacial ulcers in captive juvenile green sea turtles.

Evaluating the effects of antimicrobial drug use on the ecology of antimicrobial resistance and microbial community structure in beef feedlot cattle.

Use of antimicrobial drugs (AMDs) in food producing animals has received increasing scrutiny because of concerns about antimicrobial resistance (AMR) that might affect consumers. Previously, investigations regarding AMR have focused largely on phenotypes of selected pathogens and indicator bacteria, such as Salmonella enterica or Escherichia coli. However, genes conferring AMR are known to be distributed and shared throughout microbial communities. The objectives of this study were to employ target-enriched metagenomic sequencing and 16S rRNA gene amplicon sequencing to investigate the effects of AMD use, in the context of other management and environmental factors, on the resistome and microbiome in beef feedlot cattle. This study leveraged samples collected during a previous longitudinal study of cattle at beef feedlots in Canada. This included fecal samples collected from randomly selected individual cattle, as well as composite-fecal samples from randomly selected pens of cattle. All AMD use was recorded and characterized across different drug classes using animal defined daily dose (ADD) metrics. Overall, fecal resistome composition was dominated by genes conferring resistance to tetracycline and macrolide-lincosamide-streptogramin (MLS) drug classes. The diversity of bacterial phyla was greater early in the feeding period and decreased over time in the feedlot. This decrease in diversity occurred concurrently as the microbiome represented in different individuals and different pens shifted toward a similar composition dominated by Proteobacteria and Firmicutes. Some antimicrobial drug exposures in individuals and groups were associated with explaining a statistically significant proportion of the variance in the resistome, but the amount of variance explained by these important factors was very small (<0.6% variance each), and smaller than associations with other factors measured in this study such as time and feedlot ID. Time in the feedlot was associated with greater changes in the resistome for both individual animals and composite pen-floor samples, although the proportion of the variance associated with this factor was small (2.4% and 1.2%, respectively). Results of this study are consistent with other investigations showing that, compared to other factors, AMD exposures did not have strong effects on antimicrobial resistance or the fecal microbial ecology of beef cattle.

Dietary Supplementation with Black Raspberries Altered the Gut Microbiome Composition in a Mouse Model of Colitis-Associated Colorectal Cancer, although with Differing Effects for a Healthy versus a Western Basal Diet.

Black raspberries (BRB) are rich in anthocyanins with purported anti-inflammatory properties. However, it is not known whether dietary supplementation would ameliorate Western-diet enhanced gut inflammation and colon tumorigenesis. We employed a mouse model of colitis-associated colorectal cancer (CAC) to determine the effects of dietary supplementation with 5 to 10% (w/w) whole, freeze-dried BRB in male C57BL/6J mice fed either a standard healthy diet (AIN93G) or the total Western diet (TWD). In a pilot study, BRB suppressed colitis and colon tumorigenesis while also shifting the composition of the fecal microbiome in favor of taxa with purported health benefits, including Bifidobacterium pseudolongum. In a follow-up experiment using a 2 × 2 factorial design with AIN and TWD basal diets with and without 10% (w/w) BRB, supplementation with BRB reduced tumor multiplicity and increased colon length, irrespective of the basal diet, but it did not apparently affect colitis symptoms, colon inflammation or mucosal injury based on histopathological findings. However, BRB intake increased alpha diversity, altered beta diversity and changed the relative abundance of Erysipelotrichaceae, Bifidobacteriaceae, Streptococcaceae, Rikenellaceae, Ruminococcaceae and Akkermansiaceae, among others, of the fecal microbiome. Notably, changes in microbiome profiles were inconsistent with respect to the basal diet consumed. Overall, these studies provide equivocal evidence for in vivo anti-inflammatory effects of BRB on colitis and colon tumorigenesis; yet, BRB supplementation led to dynamic changes in the fecal microbiome composition over the course of disease development.

Metagenomics analysis of the morphological aspects and bacterial composition of broiler feces

In this descriptive study, we used metagenomics to analyze the relationship between the morphological aspects of chicken feces and its respective bacterial compositions. The microbiota composition was determined by sequencing the V4 region of the 16S rRNA genes collected from fresh broiler feces at 19 d old. In total, 48 samples were collected and divided into 8 groups of 6 samples each. The morphological changes studied were feed passage (FP) and reddish mucus (RM). Each was classified into 3 levels of intensity: 1 (slight), 2 (moderate), or 3 (intense). Thus, the 8 groups studied were feed passage (FP-1; FP-2; FP-3), reddish mucus (RM-1; RM-2; RM-3), normal ileal feces (NIF), and cecal discharge (CD). The alpha diversity (Shannon's index) revealed that the CD group showed greater diversity, and was significantly different from FP-2, FP-3, and RM-1. The beta diversity showed that the CD group samples were more homogeneous than the ileal feces groups. The relative abundance analysis revealed that Firmicutes and Proteobacteria were the most abundant phyla in the ileal feces groups. In CD, Firmicutes and Bacteroidetes were the most abundant. The relative abundance at the genus level revealed 136 different bacterial genera. In the ileal feces groups, the two most abundant genera were Lactobacillus and Escherichia/Shigella, except in the FP-1 and RM-2 groups, which had the opposite order. Unlike the others, the CD group had a higher abundance of Bacteroides and Faecalibacterium. When comparing the NIF group with the others, significant changes were found in the fecal microbiota, with nine genera for the FP groups, 19 for the RM groups, and 61 when compared to CD. The results of the present study suggest that evaluation of fecal morphology is a fundamental task that makes it possible to act quickly and assertively, as the morphological aspects of the feces may be related to the composition and structure of fecal microbiota.

Gut microbiome-wide association study of depressive symptoms

Depression is one of the most poorly understood diseases due to its elusive pathogenesis. There is an urgency to identify molecular and biological mechanisms underlying depression and the gut microbiome is a novel area of interest. Here we investigate the relation of fecal microbiome diversity and composition with depressive symptoms in 1,054 participants from the Rotterdam Study cohort and validate these findings in the Amsterdam HELIUS cohort in 1,539 subjects. We identify association of thirteen microbial taxa, including genera Eggerthella, Subdoligranulum, Coprococcus, Sellimonas, Lachnoclostridium, Hungatella, Ruminococcaceae (UCG002, UCG003 and UCG005), LachnospiraceaeUCG001, Eubacterium ventriosum and Ruminococcusgauvreauiigroup, and family Ruminococcaceae with depressive symptoms. These bacteria are known to be involved in the synthesis of glutamate, butyrate, serotonin and gamma amino butyric acid (GABA), which are key neurotransmitters for depression. Our study suggests that the gut microbiome composition may play a key role in depression.