This volume guides researchers on how to characterize, image rare, and hitherto unknown taxa and their interactions, to identify new functions and biomolecules and to understand how environmental changes condition the activity and the response of the organisms living with us and in our environment. Chapters cover different organism types (i.e., archaea, bacteria, fungi, protest, microfauna and microeukaryotes) and propose detailed protocols to produce high quality DNA, to analyse active microbial communities directly involved in complex interactions or processes through stable isotope probing, to identify and characterize of new functional genes, to image in situ interactions and to apply bioinformatics analysis tools to complex metagenomic or RNAseq sequence data. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Microbial Environmental Genomics (MEG): Methods and Protocols, Second Edition aims to serve as a primary research reference for researchers in microbiology working to in the expanding field of molecular ecology and environmental genomics.

This book addresses various aspects of in vitro digestibility: • Application of meta-analyses and machine learning methods to predict methane production; • Methane production of sainfoin and alfalfa; • In vitro evaluation of different dietary methane mitigation strategies; • Rumen methanogenesis, rumen fermentation, and microbial community response; • The role of condensed tannins in the in vitro rumen fermentation kinetics; • Fermentation pattern of several carbohydrate sources; • Additive, synergistic, or antagonistic effects of plant extracts; • In vitro rumen degradation and fermentation characteristics of silage and hay; • In vitro digestibility, in situ degradability, and rumen fermentation of camelina co-products; • Ruminal fermentation parameters and microbial matters to odd- and branched-chain fatty acids; • Comparison of fecal versus rumen inocula for the estimation of NDF digestibility; • Rumen inoculum collected from cows at slaughter or from a continuous fermenter; • Seaweeds as ingredients of ruminant diets; • Rumen in vitro fermentation and in situ degradation kinetics of forage Brassica crops; • In vitro digestibility and rumen degradability of vetch varieties; • Intestinal digestibility in vitro of Vicia sativa varieties; • Ruminal in vitro protein degradation and apparent digestibility of Pisum sativum; • In vitro digestibility studies using equine fecal inoculum; • Effects of gas production recording system and pig fecal inoculum volume on kinetics; • In vitro methods of assessing protein quality for poultry; and • In vitro techniques using the DaisyII incubator.

The second edition of the book begins with the description of the diversity of wine-related microorganisms, followed by an outline of their primary and energy metabolism. Subsequently, important aspects of the secondary metabolism are dealt with, since these activities have an impact on wine quality and off-flavour formation. Then chapters about stimulating and inhibitory growth factors follow. This knowledge is helpful for the growth management of different microbial species. The next chapters focus on the application of the consolidated findings of molecular biology and regulation the functioning of regulatory cellular networks, leading to a better understanding of the phenotypic behaviour of the microbes in general and especially of the starter cultures as well as of stimulatory and inhibitory cell-cell interactions during wine making. In the last part of the book, a compilation of modern methods complete the understanding of microbial processes during the conversion of must to wine.This broad range of topics about the biology of the microbes involved in the vinification process could be provided in one book only because of the input of many experts from different wine-growing countries.