Cultivation-Independent Analysis of the Development of the Lactobacillus spp.Community in the Intestinal Tract of Newborn Piglets

Molecular diversity and development of the Lactobacillus community in the intestinal tract, as influenced by age and intestinal compartment, were studied in one litter of 12 conventionally raised piglets. Piglets were euthanized at each week （3 animals per time）. Digesta and tissue samples from stomach, duodenum, jejunum, ileum, caecum, colon, and rectum were collected and analysed by using 16S ribosomal RNA-based methods. DGGE （denaturing gradient gel electrophoresis） profiles revealed that the Lactobacillus communities throughout the GI tract from duodenum to rectum showed good stability at same age. This indicates that fecal Lactobacillus communities can effectively represent the intestinal community. Two dominant bands were found in tissue samples of the small intestine, suggesting that the lactobacilli can adhere to the small intestinal wall. The Lactobacillus communities in different GI tract compartments developed over time. A successional change of Lactobacillus communities was observed from birth, through creep feeding to one week after weaning, showing a trend from simple to complex and back to simple. Furthermore, a clone library of Lactobacillus spp. 16S rRNA gene sequences were generated from jejunal and colonic chymes. Six dominant DGGE bands generated from jejunal chymes were matched with sequences that show 94-98% similarity to the bands derived from L. reuteri, L. delbrueckii, and L. crispatus. Seven dominant DGGE bands generated from colon chymes were matched with sequences that show 88-99% similarity to those derived from L. reuteri, L. delbrueckii, L. amylovorus/L. sobrius, and L. acidophilus. Amplicons related to L. reuteri were found in all DGGE fingerprints from jejunal digesta of age of weeks 1, 3, and 4. Amplicons related to L. amylovorus/L. sobrius were present in all DGGE fingerprints from colonic digesta of age of week 1, 3, and 4. Amplicons related to L. delbrueckii were found before weaning, L. crispatus after creep feeding before weaning and L. acidophilus after weaning. This indicates that L. reuteri and L. amylovorus/L. sobrius probably belong to the permanent composition, while L. delbruckii, L. acidophilus, and L. crispatus probably belong to the temporal groups of Lactobacillus communities in the GI tract of piglets.

Comparison of Fecal Methanogenic Archaeal Community Between Erhualian and Landrace Pigs Using Denaturing Gradient Gel Electrophoresis and Real-Time PCR Analysis

Erhualian and Landrace breeds are typical genetically obese and lean pigs, respectively. To compare the fecal methanogenic Archaeal community between these two pig breeds, fecal samples from different growth phase pigs were collected and used for PCR-denaturing gradient gel electrophoresis （DGGE） with two primer pairs （344fGC/519r and 519f/915rGC） and real-time PCR analysis. Results showed that a better separation and higher quality of bands pattern were obtained in DGGE proifles using primers 344fGC/519r as compared with primers 519f/915rGC. Sequencing of DGGE bands showed that the predominant methanogens in the feces of Erhualian and Landrace pigs belonged to Methanobrevibacter spp. and Methanosphaera spp. Real-time PCR analysis revealed that there was no signiifcant difference in the numbers of fecal total methanogens between Erhualian and Landrace pigs;however, pig growth phase affected the numbers of 16S rRNA genes of total methanogens and Methanobrevibacter smithii. Dissociation curves of methyl coenzyme-M reductase subunit A （mcrA） gene fragments ampliifed with real-time PCR showed all samples possessed a single peak at 82＆#176;C, which might be associated with M. smithii. Samples from the same growth phase of each breed showed good replicative dissociation curves. The results suggest that the growth phase （including diet factor） other than genotype of pig may affect the fecal methanogenic Archaeal community of pigs.

The dark side of technological advances in analysis of microbial ecosystems

Recent technological advances mean that samples from animal experiments may be analysed more cheaply,more easily and with a much greater return of data than previously.Research groups are frequently faced with a choice of continuing to use established technology in which they may have made a significant investment of time and resources,and have significant amounts of reference data,or switching to new technology where reference data may be limited.Apart from cost,the choice needs to be based on a comparison between the increase in data available from future experiments by switching and the value of comparison with reference data from historical experiments analysed with earlier technology.One approach to this problem is to ensure that sufficient quantity and variety of samples are taken from each experiment and appropriately stored to allow re-establishment of a sufficiently large reference set and to avoid the need to repeat animal experiments.The establishment of ‘biobanks' of experimental material will require funding for infrastructure,consistent storage of metadata and,importantly,horizon-scanning to ensure that samples are taken appropriately for techniques which will become accessible in future.Such biobanks are a recognised resource in human medicine,where the value of samples increases as more analysis is carried out and added to the metadata.

Cereal type and combined xylanase/glucanase supplementation influence the cecal microbiota composition in broilers

Dietary fiber-degrading enzyme supplementation in broilers aims at off-setting the anti-nutritive effect of non-starch polysaccharides and at promoting broiler health.Recently,we demonstrated that xylanase/glucanase addition in wheat-based diet improved nutrient digestibility,arabinoxylan fermentability and broiler growth.Conversely,maize arabinoxylan was found to be recalcitrant to xylanase action.These findings suggested that enzyme-mediated improvement of nutrient digestion and carbohydrate fermentation depended on the cereal type present in the diet,and may have contributed to broiler growth.Hence,we aimed at further investigating the link between dietary enzymes and carbohydrate fermentation in broilers,by studying the impact of enzyme supplementation in cereal-based diets,to the microbial communities in the ileum and ceca of broilers.For that purpose,96 one-day-old male broilers were randomly reared in two pens and received either wheat-based or maize-based starter and grower diets.At d 20,the broilers were randomly assigned to one out of four dietary treatments.The broilers received for 8 d the wheat-based or maize-based finisher diet as such(Control treatments;WC,MC)or supplemented with a xylanase/glucanase combination(Enzyme treatments;WE,ME).At d 28,samples from the digestive tract were collected,and the ileal and cecal microbiota composition was determined by 16S ribosomal RNA gene amplicon sequencing.A similar phylogenetic(alpha)diversity was observed among the four treatments,both in the ileal and the cecal samples.Furthermore,a similar microbial composition in the ileum(beta diversity)was observed,with lactobacilli being the predominant community for all treatments.In contrast,both cereal type and enzyme supplementation were found to influence cecal communities.The type of cereal(i.e.,wheat or maize)explained 47% of the total variation in microbial composition in the ceca.Further stratifying the analysis per cereal type revealed differences in microbiota composition between WC and WE,but not between MC and ME.Furthermore,the prevalence of beneficial genera,such as Faecalibacterium and Blautia,in the ceca of broilers fed wheat-based diets coincided with arabinoxylan accumulation.These findings indicated that fermentable arabinoxylan and arabinoxylo-oligosaccharides released by dietary xylanase may play an important role in bacterial metabolism.

Gut microbiota research nexus:One Health relationshipbetween human,animal,and environmental resistomes

The emergence and rapid spread of antimicrobial resistance is of global public health concern.The gut microbiota harboring diverse commensal and opportunistic bacteria that can acquire resistance via horizontal and vertical gene transfers is considered an important reservoir and sink of antibiotic resistance genes(ARGs).In this review,we describe the reservoirs of gut ARGs and their dynamics in both animals and humans,use the One Health perspective to track the transmission of ARG-containing bacteria between humans,animals,and the environment,and assess the impact of antimicrobial resistance on human health and socioeconomic development.The gut resistome can evolve in an environment subject to various selective pressures,including antibiotic administration and environmental and lifestyle factors(e.g.,diet,age,gender,and living conditions),and interventions through probiotics.Strategies to reduce the abundance of clinically relevant antibiotic-resistant bacteria and their resistance determinants in various environmental niches are needed to ensure the mitigation of acquired antibiotic resistance.With the help of effective measures taken at the national,local,personal,and intestinal management,it will also result in preventing or minimizing the spread of infectious diseases.This review aims to improve our understanding of the correlations between intestinal microbiota and antimicrobial resistance and provide a basis for the development of management strategies to mitigate the antimicrobial resistance crisis.