The Effect of including a Mixed-Enzyme Product in Broiler Diets on Performance, Metabolizable Energy, Phosphorus and Calcium Retention.

The importance of enzymes in the poultry industry is ever increasing because they help to extract as many nutrients as possible from the raw material available and reduce environmental impacts. Therefore, an experiment was conducted to examine the effect of a natural enzyme complex (ASC) on diets low in AME, Ca and P. Male Ross 308 broilers (n = 900) were fed one of four diets: (1) positive control (PC) with no enzyme added (AME 12.55 MJ/kg, AVPhos 4.8 g/kg and AVCal 9.6 g/kg); (2) negative control (NC) with no enzyme added and reduced AME, Ca and P (AME 12.18 MJ/kg, AVPhos 3.3 g/kg, AVCal 8.1 g/kg); (3) negative control plus ASC at 200 g/t; and (4) negative control plus ASC at 400 g/t. Broiler performance, digesta viscosity, tibia mineralization and mineral content were analyzed at d 21. Between d 18 and 20, excreted DM, GE, total nitrogen, Ca, and P were analyzed. ASC at 200 g/t and 400 g/t improved the FCR (p = 0.0014) significantly when compared with that of the NC. There were no significant differences in BW or FI between the treatments. Birds fed ASC at 200 g/t and 400 g/t had significantly improved digesta viscosity (p < 0.0001) compared with that of the PC and NC birds and had significantly higher excreted DM digestibility (p < 0.01) than the NC and the PC birds with 400 g/t ASC. ASC inclusion significantly improved P retention (p < 0.0001) compared to that in the PC. Ca retention was significantly increased by 400 g/t ASC compared to that in the PC and NC (p < 0.001). AME was significantly higher (p < 0.0001) for all treatments compared to that in the NC. There were no significant differences between treatments for any of the bone measurements. This study showed that feeding with ASC can support the performance of broilers when fed a diet formulated to have reduced Ca, P and AME, with the greatest results being seen with a higher level of ASC inclusion.

Stimbiotic supplementation and xylose-rich carbohydrates modulate broiler's capacity to ferment fibre.

Stimbiotics are a new category of feed additives that can increase fibre fermentability by stimulating fibre-degrading microbiota in the gut. The aim of this study was to test, ex vivo, if the microbiota of broilers fed a stimbiotic are better able to ferment different xylose-rich substrates in an ileal and a caecal environment. The ileal and caecal contents from broiler chickens fed a stimbiotic or from a control group were used as an inoculum in the ex vivo fermentation experiment. Different xylose-rich substrates including monomeric xylose (XYL), XOS with DP 2 to 6 (XOS), short DP XOS of 2 to 3 (sDP-XOS), long DP XOS of 4 to 6 (lDP-XOS) and de-starched wheat bran (WB), were added to each ileal and caecal inoculum in fermentation vessels. Total gas, short-chain fatty acids (SCFA) production, bacterial quantification, and carbohydrate utilisation were monitored for 9 h post-inoculation. No significant interactions were observed in any of the parameters measured in either the ileal or caecal contents (p > 0.05). Stimbiotic ileal inocula resulted in higher total gas (p < 0.001) and volatile fatty acid (VFA) (p < 0.001) production, increased numbers of Lactobacillus spp. (p < 0.001), and decreased numbers of Enterococcus spp. (p < 0.01) after 9 h regardless of the xylose-rich substrate added. Stimbiotic caecal inocula resulted in a higher ratio of VFA to branched-chain fatty acids (BCFAs) by up to +9% (p < 0.05). Ileal microbiota were found to preferentially metabolise WB, while caecal microbiota favoured XOS substrates, particularly lDP-XOS. These results indicate that stimbiotics can promote the abundance of lactic acid bacteria involved in the establishment of fibre-degrading bacteria and VFA content in the gut, which could have beneficial effects on broiler performance. Further, ileal and caecal microbiota differ in their utilisation of different substrates which may impact the effectiveness of different stimbiotic products.

Interaction between xylanase and a proton pump inhibitor on broiler chicken performance and gut function.

Three hundred thirty-six Ross 308 male broiler chicks were used in a 21-d study to explore performance and gut function when treated with a proton pump inhibitor (PPI; 0 or 89 mg/kg) in a 2 × 2 factorial arrangement with a xylanase (Xyl; 0 or 0.1 g/kg) to determine if the beneficial activity of arabinoxylan (AX) depolymerisation, through arabinoxylo-oligosaccharides (AXOS) production, starts in the upper gastrointestinal tract. Treatment with the PPI started from d 14, and by d 21 animal performance had deteriorated (P < 0.001). An interaction was observed between PPI and Xyl for feed conversion ratio (FCR) (P < 0.05), whereby the combination reduced the negative effect of PPI on FCR. Application of PPI raised digesta pH in the gizzard and caecum (P < 0.05), increased protein concentrations in the lower gut (P < 0.05) and reduced intake of digestible nutrients (P < 0.05). Caecal concentrations of indole, p-cresol, ammonia and the ratio of total volatile fatty acid (VFA) to butyric acid were increased with PPI (P < 0.05), indicating enhanced protein fermentation. Xylanase activity in the digesta were greatest in the caeca, especially when Xyl was supplemented (P < 0.001). The concentration of total soluble AX was greater in the gizzard and ileal digesta with Xyl supplementation (P < 0.05), supporting the depolymerisation action of xylanase even under acidic conditions. These data suggest xylanase may function in the gizzard even though pH is not optimal for activity and emphasises the importance of chlorohydric acid secretions in ensuring overall optimum gut function. AX depolymerisation benefits animal performance although it is still unknown how the AXOS produced with xylanase supplementation in the upper gastrointestinal tract influence the microbial populations and overall gut functionality.

The role of feed enzymes in maintaining poultry intestinal health.

Gut health or intestinal health is frequently discussed without any clear definition as to its meaning. It is suggested that this should be defined as intestinal integrity and functionality as both are a pre-requisite for the health of the intestine itself and the host. The health of the intestine is dependent upon a successful evolution of the absorptive capacity of the intestine, which in turn is influenced by the co-evolution of the intestinal immune systems and the microbiota. Nutrient supply plays a significant role in this process and from the perspective of the microbiota this changes with age as the intestines and upper gastrointestinal tract (GIT) microbiota become more effective in nutrient removal. Feed enzymes play a significant role in this process. Phytases can improve digestion of minerals, amino acids and energy and as a result reduce the availability of nutrients in the lower intestines for the microbiota. Protease can have a similar effect with amino acid supply. Non-starch polysaccharidases (NSPases) have a unique role in that they not only improve diet digestibility from the hosts perspective, thus limiting nutrient supply to the microbiota, but they also release soluble fragments of fibre from the insoluble matrix and/or depolymerize high molecular weight viscous fibre fractions in to smaller, more fermentable carbohydrate fractions. This results in a more favourable balance between fermentable carbohydrate to protein supply, a ratio which is deemed critical to maintaining good intestinal health. The dynamic nature of this complex evolution needs greater consideration if antibiotic free production is to succeed. © 2021 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Saccharomyces cerevisiae Cell Wall-Based Adsorbent Reduces Aflatoxin B1 Absorption in Rats.

Mycotoxins are naturally occurring toxins that can affect livestock health and performance upon consumption of contaminated feedstuffs. To mitigate the negative effects of mycotoxins, sequestering agents, adsorbents, or binders can be included to feed to interact with toxins, aiding their passage through the gastrointestinal tract (GI) and reducing their bioavailability. The parietal cell wall components of Saccharomyces cerevisiae have been found to interact in vitro with mycotoxins, such as, but not limited to, aflatoxin B1 (AFB1), and to improve animal performance when added to contaminated diets in vivo. The present study aimed to examine the pharmacokinetics of the absorption of radiolabeled AFB1 in rats in the presence of a yeast cell wall-based adsorbent (YCW) compared with that in the presence of the clay-based binder hydrated sodium calcium aluminosilicate (HSCAS). The results of the initial pharmacokinetic analysis showed that the absorption process across the GI tract was relatively slow, occurring over a matter of hours rather than minutes. The inclusion of mycotoxin binders increased the recovery of radiolabeled AFB1 in the small intestine, cecum, and colon at 5 and 10 h, revealing that they prevented AFB1 absorption compared with a control diet. Additionally, the accumulation of radiolabeled AFB1 was more significant in the blood plasma, kidney, and liver of animals fed the control diet, again showing the ability of the binders to reduce the assimilation of AFB1 into the body. The results showed the potential of YCW in reducing the absorption of AFB1 in vivo, and in protecting against the damaging effects of AFB1 contamination.

Efficient Aflatoxin B1 Sequestration by Yeast Cell Wall Extract and Hydrated Sodium Calcium Aluminosilicate Evaluated Using a Multimodal In-Vitro and Ex-Vivo Methodology.

In this work, adsorption of the carcinogenic mycotoxin aflatoxin B1 (AFB1) by two sequestrants-a yeast cell wall-based adsorbent (YCW) and a hydrated sodium calcium aluminosilicate (HSCAS)-was studied across four laboratory models: (1) an in vitro model from a reference method was employed to quantify the sorption capabilities of both sequestrants under buffer conditions at two pH values using liquid chromatography with fluorescence detection (LC-FLD); (2) in a second in vitro model, the influence of the upper gastrointestinal environment on the mycotoxin sorption capacity of the same two sequestrants was studied using a chronic AFB1 level commonly encountered in the field (10 µg/L and in the presence of feed); (3) the third model used a novel ex vivo approach to measure the absorption of 3H-labelled AFB1 in the intestinal tissue and the ability of the sequestrants to offset this process; and (4) a second previously developed ex vivo model readapted to AFB1 was used to measure the transfer of 3H-labelled AFB1 through live intestinal tissue, and the influence of sequestrants on its bioavailability by means of an Ussing chamber system. Despite some sorption effects caused by the feed itself studied in the second model, both in vitro models established that the adsorption capacity of both YCW and HSCAS is promoted at a low acidic pH. Ex vivo Models 3 and 4 showed that the same tested material formed a protective barrier on the epithelial mucosa and that they significantly reduced the transfer of AFB1 through live intestinal tissue. The results indicate that, by reducing the transmembrane transfer rate and reducing over 60% of the concentration of free AFB1, both products are able to significantly limit the bioavailability of AFB1. Moreover, there were limited differences between YCW and HSCAS in their sorption capacities. The inclusion of YCW in the dietary ration could have a positive influence in reducing AFB1's physiological bioavailability.

Distribution, Metabolism, and Recovery of Resin Acids in the Intestine and Tissues of Broiler Chickens in a Feeding Trial With Tall Oil Fatty Acid-Supplemented Diets.

Tall oil fatty acids (TOFA) are novel, health-improving feed ingredients which have been shown to improve the performance of broiler chickens. TOFA contains resin acids, the suggested key components for its beneficial effects. For product safety, possible accumulation of TOFA components in tissues consumed by end-users is an issue of major importance. Wheat-soy-based diets with an indigestible marker and TOFA at 0, 750 and 3,000 g/t were fed to broiler chickens for 5 weeks; 11 replicate pens/treatment. Deposition of resin acids was assessed by analyzing jejunal tissue, breast muscle, abdominal fat, blood, liver, bile, and digesta along the intestinal tract at the end of the 35-day trial. Both free and conjugated resin acids were quantified. With TOFA 3,000 g/t diet, 30% of ingested resin acids could not be recovered from jejunal digesta. Also, a proportion representing 45% of resin acids fed were in conjugated form and thus had already re-entered the intestine from the bile duct. This means that at least 75% of resin acids ingested had become absorbed in, or proximal to jejunum. Recovery of resin acids in excreta was 45 and 70% when TOFA was fed at 750 and 3,000 g/t, respectively. Based on recovery data, of the estimated 1,087 mg of resin acids ingested by birds on the high TOFA dose during their lifetime, about 330 mg was unaccounted for. In analysis of jejunal tissue, blood, liver, bile, breast muscle, and abdominal tissue, <1 mg of resin acids was found after the 35-day trial when TOFA at the 4-fold the recommended dose was fed. It is likely that the host or microbiota mineralized or converted one-third of resin acids to a form that escaped analysis. TOFA at 3,000 g/t dose caused no detectable adverse effects in broiler chickens. Based on analysis of breast meat and liver, the common edible tissues, a human consumer would ingest <100 µg of resin acids in a single meal. That is one-thousandth of the dose shown to be harmless in rodents. Thus, unintentional exposure of human consumers to resin acids is marginal, and posed no safety concerns.

Design and validation of a real-time PCR technique for assessing the level of inclusion of fungus- and yeast-based additives in feeds.

A reliable method for quantification of non-viable microbe-based nutritional and zootechnical additives introduced into feed is essential in order to ensure regulatory compliance, feed safety and product authenticity in industrial applications. In the present work, we developed a novel real-time quantitative polymerase chain reaction (qPCR) -based analysis protocol for monitoring two microbial additives in feed matrices. To evaluate the applicability of the method, pelleted wheat- and maize-based broiler chicken diets containing a non-viable phytase-producing strain of Aspergillus niger produced in solid state fermentation (150 or 300 g/t) and a non-viable selenium-enriched Saccharomyces cerevisiae (100 or 200 g/t) as model feed ingredients, were manufactured and subjected to analysis. Power analysis of the qPCR results indicated that 2 to 6 replicate feed samples were required to distinguish the product doses applied, which confirms that the microbial DNA was efficiently recovered and that potential PCR inhibitors present in the feed material were successfully removed in DNA extraction. The analysis concept described here was shown to be an accurate and sensitive tool for monitoring the inclusion levels of non-viable, unculturable microbial supplements in animal diets.

Comprehensive Evaluation of the Efficiency of Yeast Cell Wall Extract to Adsorb Ochratoxin A and Mitigate Accumulation of the Toxin in Broiler Chickens.

Ochratoxin A (OTA) is a common mycotoxin contaminant in animal feed. When absorbed from the gastrointestinal tract, OTA has a propensity for pathological effects on animal health and deposition in animal tissues. In this study, the potential of yeast cell wall extracts (YCWE) to adsorb OTA was evaluated using an in vitro method in which consecutive animal digestion events were simulated. Low pH markedly increased OTA binding to YCWE, which was reversed with a pH increased to 6.5. Overall, in vitro analysis revealed that 30% of OTA was adsorbed to YCWE. Additional computational molecular modelling revealed that change in pH alters the OTA charge and modulates the interaction with the YCWE ß-D-glucans. The effectiveness of YCWE was tested in a 14-day broiler chicken trial. Birds were subjected to five dietary treatments; with and without OTA, and OTA combined with YCWE at three dosages. At the end of the trial, liver OTA deposition was evaluated. Data showed a decrease of up to 30% in OTA deposits in the liver of broilers fed both OTA and YCWE. In the case of OTA, a tight correlation between the mitigation efficacy of YCWE between in vitro and in vivo model could be observed.

Conversion of Branched-Chain Amino Acids to Corresponding Isoacids - An in vitro Tool for Estimating Ruminal Protein Degradability.

In this paper we describe a study that evaluates the applicability of an in vitro fermentation model to assess the resistance of protein supplements to rumen degradation. The protein sources used were: soybean meal (SBM); whey protein (WHEY), which was expected to be rapidly degraded, and yeast-derived microbial protein (YMP), which was proposed to be resistant to rumen degradation. The basal diet was composed of grass silage and a commercial compound feed. The protein supplements were added at three isonitrogenous doses. Fermentation was monitored for 24 h and gas production, volatile fatty acids, lactic acid, and ammonia were analyzed at three timepoints. Protein degradation was estimated by determining the extent to which branched-chain amino acids (BCAA) introduced with the protein supplement were converted to corresponding branched-chain volatile fatty acids (BCVFA). At the highest dose of WHEY, 60% of introduced valine, leucine, and isoleucine was recovered as isobutyric, 2-methylbutyric, and isovaleric acid (products of BCAA decarboxylation and deamination), respectively. The BCVFA detected represented 50% of added BCAA with SBM, but <15% with YMP. Further indications that YMP protein is resistant to degradation were provided by analysis of ammonia. With YMP, the residual ammonia concentration only marginally exceeded that of the cultures with no protein supplementation, while it increased dose-dependently when the vessels were supplemented with WHEY or SBM. This suggests that with WHEY and SBM, the rate of deamination exceeded the rate of ammonia assimilation by bacteria. Residual ammonia and BCVFA, the two indicators of protein fermentation, were strongly correlated. Overall bacterial activity was monitored as yield of gas, volatile fatty acids, and bacteria. These three correlating parameters showed that WHEY only modestly stimulated fermentation, whereas SBM and YMP stimulated fermentation extensively, possibly owing to their higher carbohydrate content. The results presented suggest that the in vitro fermentation method was suitable for detecting differences in resistance of protein supplements to rumen degradation and following a full method validation could be a useful tool for diet formulation. The data obtained suggested that YMP was the most resistant and WHEY the most susceptible to degradation.

The impact of Bacillus subtilis DSM 32315 on the pathology, performance, and intestinal microbiome of broiler chickens in a necrotic enteritis challenge.

It was hypothesized that dietary inclusion of Bacillus subtilis DSM 32315 could inhibit Clostridium perfringens induced necrotic enteritis (NE), thereby improving broiler performance. Male, d 0 chicks were randomly assigned 14 birds/pen, 11 pens/treatment in 3 treatments: a basal diet (control), a coccidiostat fed control (Narasin), and a direct fed microbial (DFM) B. subtilis DSM 32315 treatment. Necrotic enteritis was induced in all birds by oral inoculation of Eimeria maxima oocysts on d 12 and a virulent C. perfringens on d 16. Mortality was reduced (P < 0.001) in DFM and Narasin compared to control. DFM reduced (P < 0.001) feed conversion ratio (FCR) compared to control. Furthermore, DFM and Narasin reduced (P < 0.001) footpad lesions. The DFM was shown to increase (P < 0.05) Bacillus spp. and decrease (P < 0.05) C. perfringens in the ileum and cecum at several time points. To investigate microbiome changes in the cecum, digesta samples were analyzed with % guanine and cytosine (%G+C) microbial profiling which fractionates bacterial chromosomes based on the %G+C in DNA. The method revealed treatment profile peaks in low (27.0 to 34.5%), mid (40.5 to 54.0%), and high (59.0 to 68.0%) G+C fractions. 16S rRNA gene amplification and high throughput sequencing was conducted on each of these fractions in order to elucidate specific bacterial population differences. In the low and mid %G+C fractions, DFM had greater abundance of Lactobacillaceae family members (P = 0.03 and P = 0.01, respectively) and Lactobacillus salivarius (P = 0.04 and P = 0.01, respectively) than control or Narasin. Lactobacillus johnsonii was also greater in the low %G+C fraction compared to control and Narasin (P = 0.01). Lachnospiraceae (P = 0.04) and Ruminococcaceae (P < 0.01) in the mid %G+C fraction were reduced in the DFM compared to control. Positive alterations to the microbial populations in the gut of broilers may at least be a partial mechanism by which B. subtilis DSM 32315 reduced pathology and improved performance of broilers in the NE challenge.

Effect of high contents of dietary animal-derived protein or carbohydrates on canine faecal microbiota.

BACKGROUND: Considerable evidence suggests that food impacts both the gastro-intestinal (GI) function and the microbial ecology of the canine GI tract. The aim of this study was to evaluate the influence of high-carbohydrate (HC), high-protein (HP) and dry commercial (DC) diets on the canine colonic microbiota in Beagle dogs. Diets were allocated according to the Graeco-Latin square design. For this purpose, microbial DNA was isolated from faecal samples and separated by density gradient centrifugation, resulting in specific profiling based on the guanine-cytosine content (%G+C). In addition, 16 S rRNA gene amplicons were obtained from the most abundant %G + C peaks and analysed by sequence analysis, producing a total of 720 non-redundant sequences (240 sequences per diet). RESULTS: The DC diet sample showed high abundance of representatives of the orders Clostridiales, Lactobacillales, Coriobacteriales and Bacteroidales. Sequence diversity was highest for DC diet samples and included representatives of the orders Lactobacillales and Bacteroidales, which were not detected in samples from the HP and HC diets. These latter two diets also had reduced levels of representatives of the family Lachnospiraceae, specifically Clostridial cluster XIVa. The HC diet favoured representatives of the order Erysipelotrichales, more specifically the Clostridial cluster XVIII, while the HP diet favoured representatives of the order Fusobacteriales. CONCLUSIONS: This study detected Coriobacteriales in dog faeces, possibly due to the non-selective nature of the %G + C profiling method used in combination with sequencing. Moreover, our work demonstrates that the effect of diet on faecal microbiota can be explained based on the metabolic properties of the detected microbial taxa.

A novel polymyxin derivative that lacks the fatty acid tail and carries only three positive charges has strong synergism with agents excluded by the intact outer membrane.

Polymyxins are cationic lipopeptides (five cationic charges) and the last resort for the treatment of serious Gram-negative infections caused by multiresistant strains. NAB741 has a cyclic peptide portion identical to that of polymyxin B but carries in the linear peptide portion a threonyl-D-serinyl residue (no cationic charges) instead of the diaminobutyryl-threonyl-diaminobutyryl residue (two cationic charges). At the N terminus of the peptide, NAB741 carries an acetyl group instead of a mixture of methyl octanoyl and methyl heptanoyl residues. NAB741 sensitized Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae, and Acinetobacter baumannii to antibiotics against which the intact outer membrane is an effective permeability barrier. When tested by using Etest strips on plates containing increasing concentrations of NAB741, the fractional inhibition concentration index (FICI) of the combination of NAB741 with rifampin ranged from

Susceptibility of carbapenemase-producing strains of Klebsiella pneumoniae and Escherichia coli to the direct antibacterial activity of NAB739 and to the synergistic activity of NAB7061 with rifampicin and clarithromycin.

OBJECTIVES: To determine the susceptibility of carbapenemase-producing strains of Klebsiella pneumoniae and Escherichia coli to the direct antibacterial activity of NAB739 and to the synergistic activity of NAB7061 with rifampicin and clarithromycin. NAB739 and NAB7061 are novel polymyxin derivatives that lack the cationic charges in the linear peptide portion of polymyxin B and have pharmacokinetic properties different from those of polymyxin B. METHODS: MIC determinations were performed by the agar dilution method using CLSI guidelines. Polymyxin B was used as a comparison. Synergism studies measured fractional inhibitory concentration indices (FICIs) by using increasing concentrations of the compounds in Mueller-Hinton agar and Etests. RESULTS: The MICs of NAB739 for all nine polymyxin-susceptible, carbapenemase-producing strains were identical or very close to those determined for E. coli ATCC 25922, for K. pneumoniae ATCC 13883, as well as for 18 clinical carbapenem-susceptible isolates. At a concentration of 4 mg/L, NAB7061 decreased the MIC of rifampicin and clarithromycin for all carbapenemase strains by factors ranging from 6 to 500. The polymyxin-resistant strain K. pneumoniae CL5762B was sensitized by a factor of 24 to rifampicin (FICI, 0.167) and by a factor of 12 to clarithromycin (FICI, 0.208). CONCLUSIONS: Polymyxin-susceptible, carbapenemase-producing strains are as susceptible to NAB739 as are the carbapenem-susceptible clinical isolates. In addition, NAB7061 has notable synergism with rifampicin and clarithromycin against all the carbapenemase-producing strains tested, including the polymyxin-resistant K. pneumoniae strain.

Characterization of microbial contaminants in urine.

Modern, molecular microbiological methods were applied to urine samples from control subjects and athletes for characterization of the microbial community. High abundance of lactobacilli, enterococci, and enterobacteria was detected in urine samples, suggesting that gastrointestinal and urogenital tracts act as contamination sources. Athlete samples, but not control samples, showed an abundance of pseudomonads, a bacterial group reported to metabolize steroids. Overall, the bacteria detected are known to be capable of altering steroid profiles, emphasizing the importance of good hygiene at sampling in reliable doping control.

Worldwide prevalence of class 2 integrases outside the clinical setting is associated with human impact.

An intI-targeted PCR assay was optimized to evaluate the frequency of partial class 2-like integrases relative to putative, environmental IntI elements in clone libraries generated from 17 samples that included various terrestrial, marine, and deep-sea habitats with different exposures to human influence. We identified 169 unique IntI phylotypes (< or =98% amino acid identity) relative to themselves and with respect to those previously described. Among these, six variants showed an undescribed, extended, IntI-specific additional domain. A connection between human influence and the dominance of IntI-2-like variants was also observed. IntI phylotypes 80 to 99% identical to class 2 integrases comprised approximately 70 to 100% (n = 65 to 87) of the IntI elements detected in samples with a high input of fecal waste, whereas IntI2-like sequences were undetected in undisturbed settings and poorly represented (1 to 10%; n = 40 to 79) in environments with moderate or no recent fecal or anthropogenic impact. Eleven partial IntI2-like sequences lacking the signature ochre 179 codon were found among samples of biosolids and agricultural soil supplemented with swine manure, indicating a wider distribution of potentially functional IntI2 variants than previously reported. To evaluate IntI2 distribution patterns beyond the usual hosts, namely, the Enterobacteriaceae, we coupled PCR assays targeted at intI and 16S rRNA loci to G+C fractionation of total DNA extracted from manured cropland. IntI2-like sequences and 16S rRNA phylotypes related to Firmicutes (Clostridium and Bacillus) and Bacteroidetes (Chitinophaga and Sphingobacterium) dominated a low-G+C fraction ( approximately 40 to 45%), suggesting that these groups could be important IntI2 hosts in manured soil. Moreover, G+G fractionation uncovered an additional set of 36 novel IntI phylotypes (< or =98% amino acid identity) undetected in bulk DNA and revealed the prevalence of potentially functional IntI2 variants in the low-G+C fraction.

Shotgun metaproteomics of the human distal gut microbiota.

The human gut contains a dense, complex and diverse microbial community, comprising the gut microbiome. Metagenomics has recently revealed the composition of genes in the gut microbiome, but provides no direct information about which genes are expressed or functioning. Therefore, our goal was to develop a novel approach to directly identify microbial proteins in fecal samples to gain information about the genes expressed and about key microbial functions in the human gut. We used a non-targeted, shotgun mass spectrometry-based whole community proteomics, or metaproteomics, approach for the first deep proteome measurements of thousands of proteins in human fecal samples, thus demonstrating this approach on the most complex sample type to date. The resulting metaproteomes had a skewed distribution relative to the metagenome, with more proteins for translation, energy production and carbohydrate metabolism when compared to what was earlier predicted from metagenomics. Human proteins, including antimicrobial peptides, were also identified, providing a non-targeted glimpse of the host response to the microbiota. Several unknown proteins represented previously undescribed microbial pathways or host immune responses, revealing a novel complex interplay between the human host and its associated microbes.

Novel polymyxin derivatives carrying only three positive charges are effective antibacterial agents.

The lack of novel antibiotics against gram-negative bacteria has reinstated polymyxins as the drugs of last resort to treat serious infections caused by extremely multiresistant gram-negative organisms. However, polymyxins are nephrotoxic, and this feature may complicate therapy or even require its discontinuation. Like that of aminoglycosides, the nephrotoxicity of polymyxins might be related to the highly cationic nature of the molecule. Colistin and polymyxin B carry five positive charges. Here we show that novel polymyxin derivatives carrying only three positive charges are effective antibacterial agents. NAB739 has a cyclic peptide portion identical to that of polymyxin B, but in the linear portion of the peptide, it carries the threonyl-D-serinyl residue (no cationic charges) instead of the diaminobutyryl-threonyl-diaminobutyryl residue (two cationic charges). The MICs of NAB739 for 17 strains of Escherichia coli were identical, or very close, to those of polymyxin B. Furthermore, NAB739 was effective against other polymyxin-susceptible strains of Enterobacteriaceae and against Acinetobacter baumannii. At subinhibitory concentrations, it dramatically sensitized A. baumannii to low concentrations of antibiotics such as rifampin, clarithromycin, vancomycin, fusidic acid, and meropenem. NAB739 methanesulfonate was a prodrug analogous to colistin methanesulfonate. NAB740 was the most active derivative against Pseudomonas aeruginosa. NAB7061 (linear portion of the peptide, threonyl-aminobutyryl) lacked direct antibacterial activity but sensitized the targets to hydrophobic antibiotics by factors up to 2,000. The affinities of the NAB compounds for isolated rat kidney brush border membrane were significantly lower than that of polymyxin B.

Molecular analysis of the gut microbiota of identical twins with Crohn's disease.

Increasing evidence suggests that a combination of host genetics and the composition of the gut microbiota are important for development of Crohn's disease (CD). Our aim was to study identical twins with CD to determine microbial factors independent of host genetics. Fecal samples were studied from 10 monozygotic twin pairs with CD (discordant n=6 and concordant n=4) and 8 healthy twin pairs. DNA was extracted, 16S rRNA genes were PCR amplified and T-RFLP fingerprints generated using general bacterial and Bacteroides group-specific primers. The microbial communities were also profiled based on their percentage G+C contents. Bacteroides 16S rRNA genes were cloned and sequenced from a subset of the samples. The bacterial diversity in each sample and similarity indices between samples were estimated based on the T-RFLP data using a combination of statistical approaches. Healthy individuals had a significantly higher bacterial diversity compared to individuals with CD. The fecal microbial communities were more similar between healthy twins than between twins with CD, especially when these were discordant for the disease. The microbial community profiles of individuals with ileal CD were significantly different from healthy individuals and those with colonic CD. Also, CD individuals had a lower relative abundance of B. uniformis and higher relative abundances of B. ovatus and B. vulgatus. Our results suggest that genetics and/or environmental exposure during childhood, in part, determine the gut microbial composition. However, CD is associated with dramatic changes in the gut microbiota and this was particularly evident for individuals with ileal CD.

Identification of the most abundant lactobacillus species in the crop of 1- and 5-week-old broiler chickens.

Bacteria from crops of 1- and 5-week-old broiler chickens fed with two brands (diets A and B) of wheat-based diets were isolated on Lactobacillus-selective medium and identified (n = 300) based on partial 16S rRNA gene sequence. The most abundant Lactobacillus species were L. reuteri (33%), L. crispatus (18.7%), and L. salivarius (13.3%). Regardless of farm and feed, L. reuteri was the most abundant species (P < 0.005) in the crops of the younger chickens. However, the amount of L. reuteri was significantly reduced in the crops of the 5-week-old chickens regardless of the feed (P = 0.016). The diversity of L. reuteri isolates was studied by fatty acid analysis, and the 94 L. reuteri isolates could be arranged into several clusters. The nisin sensitivities of the L. reuteri isolates were determined because nisin is a candidate coccidiostat. Sensitive isolates were found more frequently in younger chickens (77%) than in 5-week-old chickens (23%), whereas chickens fed with commercial feed B had a higher proportion of nisin-resistant isolates (73%) than did chickens fed with feed A (45%). Nisin-resistant strains are potential candidates for adjunct cultures for maintaining L. reuteri in its natural niche in the crop and are potential targets for genetic engineering with nisin-selectable food-grade vectors. The diversity of the L. reuteri population suggested that one should consider including several strains representing different clusters and nisin resistance phenotypes in candidate probiotic feed supplements for chickens.