Concentration and chemical form of dietary zinc shape the porcine colon microbiome, its functional capacity and antibiotic resistance gene repertoire.

Despite a well-documented effect of high dietary zinc oxide on the pig intestinal microbiota composition less is it yet known about changes in microbial functional properties or the effect of organic zinc sources. Forty weaning piglets in four groups were fed diets supplemented with 40 or 110 ppm zinc as zinc oxide, 110 ppm as Zn-Lysinate, or 2500 ppm as zinc oxide. Host zinc homeostasis, intestinal zinc fractions, and ileal nutrient digestibility were determined as main nutritional and physiological factors putatively driving colon microbial ecology.

Lythrum salicaria L. herb and gut microbiota of healthy post-weaning piglets. Focus on prebiotic properties and formation of postbiotic metabolites in ex vivo cultures.

Ethnopharmacological Relevance: Herb of purple loosestrife (Lythrum salicaria L. from Lythraceae family) (LSH) was used in Europe since ancient times till early-20th century in the therapy of diarrhea and dysentery in human and veterinary medicine. Post-weaning diarrhea is a main problem affecting global piglet production, which leads to significant economic losses because of increased morbidity and mortality, reduced average daily gain, and high antibiotic consumption.

ganon: precise metagenomics classification against large and up-to-date sets of reference sequences.

Motivation: The exponential growth of assembled genome sequences greatly benefits metagenomics studies. However, currently available methods struggle to manage the increasing amount of sequences and their frequent updates. Indexing the current RefSeq can take days and hundreds of GB of memory on large servers.

Developing Gut Microbiota Exerts Colonisation Resistance to syn. in Piglets.

(syn. ) is considered a pioneer colonizer and may cause gut infection in neonatal piglets. The aim of this study was to explore the microbiota- associations in pigs.

DREAM-Yara: an exact read mapper for very large databases with short update time.

Motivation: Mapping-based approaches have become limited in their application to very large sets of references since computing an FM-index for very large databases (e.g. >10 GB) has become a bottleneck.

Formula Feeding Predisposes Neonatal Piglets to Clostridium difficile Gut Infection.

Spontaneous outbreaks of Clostridium difficile infection (CDI) occur in neonatal piglets, but the predisposing factors are largely not known. To study the conditions for C. difficile colonization and CDI development, 48 neonatal piglets were moved into isolators, fed bovine milk-based formula, and infected with C.

The SeqAn C++ template library for efficient sequence analysis: A resource for programmers.

Background: The use of novel algorithmic techniques is pivotal to many important problems in life science. For example the sequencing of the human genome (Venter et al., 2001) would not have been possible without advanced assembly algorithms and the development of practical BWT based read mappers have been instrumental for NGS analysis.

SLIMM: species level identification of microorganisms from metagenomes.

Identification and quantification of microorganisms is a significant step in studying the alpha and beta diversities within and between microbial communities respectively. Both identification and quantification of a given microbial community can be carried out using whole genome shotgun sequences with less bias than when using 16S-rDNA sequences. However, shared regions of DNA among reference genomes and taxonomic units pose a significant challenge in assigning reads correctly to their true origins.