Invited review: Application of meta-omics to understand the dynamic nature of the rumen microbiome and how it responds to diet in ruminants

Ruminants are unique among livestock due to their ability to efficiently convert plant cell wall carbohydrates into meat and milk. This ability is a result of the evolution of an essential symbiotic association with a complex microbial community in the rumen that includes vast numbers of bacteria, methanogenic archaea, anaerobic fungi and protozoa. These microbes produce a diverse array of enzymes that convert ingested feedstuffs into volatile fatty acids and microbial protein which are used by the animal for growth. Recent advances in high-throughput sequencing and bioinformatic analyses have helped to reveal how the composition of the rumen microbiome varies significantly during the development of the ruminant host, and with changes in diet. These sequencing efforts are also beginning to explain how shifts in the microbiome affect feed efficiency. In this review, we provide an overview of how meta-omics technologies have been applied to understanding the rumen microbiome, and the impact that diet has on the rumen microbial community.     

Diversity of extremely halophilic bacteria

In this review, the history of the classification of the family Halobacteriaceae, the extremely halophilic aerobic Archaea, is reviewed with some emphasis on the recently described new genera Halobaculum, Halorubrum, Natrialba, Natronomonas, and "Haloterrigena." Speculation is made about the evolutionary relationship between members of the Halobacteriaceae and the extremely halophilic, anaerobic methanogens of the genera Methanohalobium and Methanohalophilus. Efforts to find missing links between the two groups are also reviewed. Received: January 22, 1998 / Accepted: February 16, 1998     

Application of Meta-Mesh on the analysis of microbial communities from human associated-habitats

With the current fast accumulation of microbial community samples and related metagenomic sequencing data, data integration and analysis system is urgently needed for in-depth analysis of large number of metagenomic samples (also referred to as “microbial communities”) of interest. Although several existing databases have collected a large number of metagenomic samples, they mostly serve as data repositories with crude annotations, and offer limited functionality for analysis. Moreover, the few available tools for comparative analysis in the literature could only support the comparison of a few pre-defined set of metagenomic samples. To facilitate comprehensive comparative analysis on large amount of diverse microbial community samples, we have designed a Meta-Mesh system for a variety of analyses including quantitative analysis of similarities among microbial communities and computation of the correlation between the meta-information of these samples. We have used Meta-Mesh for systematically and efficiently analyses on diverse sets of human associate-habitat microbial community samples. Results have shown that Meta-Mesh could serve well as an efficient data analysis platform for discovery of clusters, biomarker and other valuable biological information from a large pool of human microbial samples.     

Denitrification by extremely halophilic bacteria

Abstract Extremely halophilic bacteria were isolated from widely separated sites by anaerobic enrichment in the presence of nitrate. The anaerobic growth of several of these isolates was accompanied by the production of nitrite, nitrous oxide, and dinitrogen. These results are a direct confirmation of the existence of extremely halophilic denitrifying bacteria, and suggest that such bacteria may be common inhabitants of hypersaline environments.     

Substrate uptake in extremely halophilic microbial communities revealed by microautoradiography and fluorescence in situ hybridization

The combination of fluorescence in situ hybridization and microautoradiography (FISH-MAR approach) was applied to brine samples of a solar saltern crystallizer pond from Mallorca (Spain) where the simultaneous occurrence of Salinibacter spp. and the conspicuous square Archaea had been detected. Radioactively labeled bicarbonate, acetate, glycerol, and an amino acid mixture were tested as substrates for the microbial populations inhabiting such brines. The results indicated that hitherto uncultured 'square Archaea' do actively incorporate amino acids and acetate. However, Salinibacter spp. only showed amino acid incorporation in pure culture, but no evidence of such activity in their natural environment could be demonstrated. No glycerol incorporation was observed for any component of the microbial community.Communicated by W.D. Grant     

The ecology of the extremely halophilic archaea

Abstract: The extremely halophilic archaea (family Halobacteriaceae) are the dominant heterotrophic organisms in hypersaline environments in which salt concentrations exceed 250–300 g l⁻¹. During the last decades our knowledge on the taxonomy, physiology and biochemistry of the Halobacterium group has greatly increased. However, our understanding of the ecology of the halophilic archaea lags far behind the progess made in the study of other aspects of their biology. A few hypersaline environments, such as the Dead Sea and solar salterns, have been studied more in depth, using techniques such as lipid analysis to obtain information on the types of organisms present and measurement of uptake of labeled substrates to quantify the dynamics of bacterial processes. The results of these studies, in combination with the information obtained from laboratory studies of representative isolates of the Halobacteriaceae, enable the beginning of an understanding of the functioning of the halophilic archaea in nature.     

DNA base composition of extremely halophilic cocci

Summary The percentage guanine+cytosine (GC) content of the DNA of 9 extremely halophilic cocci were determined from melting temperature (T _m) and the E ₂₆₀/E ₂₈₀ ratio at pH 3. The values found ranged from 60.5–65.8, with an average 62.6% GC.     

Tolerance of extremely halophilic archaebacteria towards bromide

The tolerance of halophilic archaebacteria towards bromide was tested in view of the fact that bromide occurs in natural brines in concentrations of up to 66 mM. It was found that, while concentrations of up to 0.8–1M are tolerated well by all halobacterial types examined, great differences exist between species with respect to bromide tolerance. WhileHalobacterium (H. salinarium, H. halobium, andH. sodomense) andNatronobacterium species are only moderately tolerant,Haloarcula (H. vallismortis, H. marismortui), andHaloferax species (H. mediterranei, H. gibbonsii) tolerate higher concentrations.Haloferax volcanii proved extremely tolerant and showed growth in bromide media at very low chloride concentrations (below 50 mM). No correlation was found between bromide tolerance and the bromide concentration in the habitat from which the strains were isolated. Iodide proved much more toxic than bromide. Bromide-tolerant strains also proved relatively resistant to growth inhibition by iodide.     

Cell wall of an extremely halophilic coccus

Summary Amino acid and amino sugar analyses have been carried out on hydrolyzed wall preparations from an extremely halophilic coccus. A limited number of ninhydrin-positive compounds were found. The amino acids glycine and glutamic acid or glutamine were present, as well as the amino sugars glucosamine and galactosamine. In addition, three unidentified compounds were detected. Other peptidoglycan components, as found in non-halophilic Gram-positive cocci, were absent.     

Cytological peculiarities of some extremely halophilic soil archaeobacteria

Ultrastructure and morphogenesis of extremely halophilic neutrophilic (Halobacteriam distributum, Halococcus turkmenicus) and alkaliphilic (Natronobacterium pharaonis, Natronococcus occultus) archaeobacteria were studied. The H. distributum culture was rather polymorphous and produced cells of four types. Due to the irregular cell fission in different planes packages of various numbers of cells surrounded by a common capsule were formed. Resting forms (halocysts) with multilayer covers were present in the population. The N. pharaonis culture consisted of rod-like cells and cyst-like forms. Besides, under conditions of carbon limitation, multicellular aggregated forms were found in the culture. Encapsulated single cells and aggregated forms with a common capsule were observed in H. turkmenicus and N. occultus cultures.     

The occurrence of denitrification in extremely halophilic bacteria

Abstract A total of 97 aerobic and facultatively anaerobic bacteria, and 3 Candida albicans , were tested for their ability to inhibit the growth of Haemophilus influenzae . Only strains of Pseudomonas aeruginosa showed any inhibitory effect and all 5 strains tested clearly inhibited the growth of all 10 strains of H. influenzae . The inhibition of H. influenzae . by Ps. aeruginosa may play a role in the establishment of chronic Ps. aeruginosa infections in the respiratory tracts of patients with bronchiectasis and cystic fibrosis (CF).