The Pathology of Methanogenic Archaea in Human Gastrointestinal Tract Disease

Methane-producing archaea have recently been associated with disorders of the gastrointestinal tract and dysbiosis of the resident microbiota. Some of these conditions include inflammatory bowel disease (Crohn’s disease (CD) and ulcerative colitis (UC)), chronic constipation, small intestinal bacterial overgrowth, gastrointestinal cancer, anorexia, and obesity. The causal relationship and the putative mechanism by which archaea may be associated with human disease are poorly understood, as are the strategies to alter methanogen populations in humans. It is estimated that 30–62% of humans produce methane detectable in exhaled breath and in the gastrointestinal tract. However, it is not yet known what portion of the human population have detectable methanogenic archaea. Hydrogen and methane are often measured in the breath as clinical indicators of intolerance to lactose and other carbohydrates. Breath gas analysis is also employed to diagnose suspected small intestinal bacterial overgrowth and irritable bowel syndrome, although standards are lacking. The diagnostic value for breath gas measurement in human disease is evolving; therefore, standardized breath gas measurements combined with ever-improving molecular methodologies could provide novel strategies to prevent, diagnose, or manage numerous colonic disorders. In cases where methanogens are potentially pathogenic, more data are required to develop therapeutic antimicrobials or other mitigation strategies

Microorganisms in the rumen and reticulum of buffalo (Bubalus bubalis) fed two different feeding systems

Abstract\ud \ud Background\ud The community of microorganisms in the rumen and reticulum is influenced by feeding as well as the species and geographical distribution of ruminant animals. Bacteria, methanogenic archaea and ciliate protozoa existing in the rumen and reticulum were evaluated by real-time polymerase chain reaction and light microscopy in buffalo in two feeding systems, grazing and feedlot.\ud \ud \ud Results\ud No significant differences were observed in the total concentrations of bacteria/mL and archaea between rumen and reticulum, and between pasture and feedlots, or interactions between variables. However, the largest density of bacteria and smallest density of archaea was observed in the rumen of grazing animals. The total ciliates protozoa community was higher in grazing buffalo than those in the feedlot on a concentrated diet. There were significant interactions between location in the gastrointestinal tract (rumen vs reticulum) and types of diets (grazing vs feedlot) in the composition of ciliates.\ud \ud \ud Conclusions\ud Our data showed differences in the microbial community of the rumen and reticulum between grazing and feedlot feeding systems demonstrating relevant changes in the microorganism:host relationship existing on rumen–reticulum ecosystem.This work was supported by the Conselho Nacional de Desenvolvimento\ud Científico e Tecnologico (CNPq) from Federal Government of Brazil

Parallel evolution of histophagy in ciliates of the genus Tetrahymena

BACKGROUND: Species of Tetrahymena were grouped into three complexes based on morphological and life history traits: the pyriformis complex of microstomatous forms; the patula complex of microstome-macrostome transformers; and the rostrata complex of facultative and obligate histophages. We tested whether these three complexes are paraphyletic using the complete sequence of the small subunit rDNA (SSrDNA). RESULTS: In addition to the 16 species of Tetrahymena whose SSrDNA sequences are known, we sequenced the complete SSrDNA from the following histophagous Tetrahymena species; Tetrahymena bergeri, Tetrahymena mobilis, Tetrahymena rostrata, and Tetrahymena setosa as well as the macrostome species Tetrahymena vorax. We also included a ciliate tentatively identified as Lambornella sp., a parasite of the mosquito Aedes sp. We confirmed earlier results using SSrDNA, which showed two distinct clusters of Tetrahymena species: the australis group and borealis group. The genetic distances among Tetrahymena are in general very small. However, all nodes were supported by high bootstrap values. With the exception of T. bergeri and T. corlissi, which are both histophagous and group as sister species, all other histophagous Tetrahymena species are most closely related to a bacterivorous species. Furthermore, Lambornella sp. and T. empidokyrea, both mosquito parasites, are sister species, although there is a considerable genetic distance between them. CONCLUSIONS: There has been parallel evolution of histophagy in the genus Tetrahymena and the three classical species complexes are paraphyletic. As the genus Lambornella arises within the Tetrahymena clade, it is not likely a defensible one

Influence of periparturient and postpartum diets on rumen methanogen communities in three breeds of primiparous dairy cows

Background: Enteric methane from rumen methanogens is responsible for 25.9 % of total methane emissions in the United States. Rumen methanogens also contribute to decreased animal feed efficiency. For methane mitigation strategies to be successful, it is important to establish which factors influence the rumen methanogen community and rumen volatile fatty acids (VFA). In the present study, we used next-generation sequencing to determine if dairy breed and/or days in milk (DIM) (high-fiber periparturient versus high-starch postpartum diets) affect the rumen environment and methanogen community of primiparous Holstein, Jersey, and Holstein-Jersey crossbreeds. Results: When the 16S rRNA gene sequences were processed and assigned to operational taxonomic units (OTU), a core methanogen community was identified, consisting of Methanobrevibacter (Mbr.) smithii, Mbr. thaueri, Mbr. ruminantium, and Mbr. millerae. The 16S rRNA gene sequence reads clustered at 3 DIM, but not by breed. At 3 DIM, the mean % abundance of Mbr. thaueri was lower in Jerseys (26.9 %) and higher in Holsteins (30.7 %) and Holstein-Jersey crossbreeds (30.3 %) (P < 0.001). The molar concentrations of total VFA were higher at 3 DIM than at 93, 183, and 273 DIM, whereas the molar proportions of propionate were increased at 3 and 93 DIM, relative to 183 and 273 DIM. Rumen methanogen densities, distributions of the Mbr. species, and VFA molar proportions did not differ by breed. Conclusions: The data from the present study suggest that a core methanogen community is present among dairy breeds, through out a lactation. Furthermore, the methanogen communities were more influenced by DIM and the breed by DIM interactions than breed differences.The author's would like to acknowledge the USDA Hatch Grant (VT-H01801) and the UVM Dairy Center of Excellence as funding sources for animals and laboratory supplies. Furthermore, the Agriculture and Food Research Initiative Competitive Grant no. 2014-67016-21791 from the USDA National Institute of Food and Agriculture supported the VFA and feed analyses. We would like to thank Dr. Benoit St-Pierre of South Dakota State University for assistance with bioinformatics and Kurt Cotanch of the William H. Miner Institute for assistance with VFA analyses. We would also like to thank the Paul Miller Research Farm staff (Matt Boudette, Scott Shumway, Doug Watkin) for their on-farm maintenance and assistance. Lastly, we would like to thank Columbia University undergraduate student, Ryan C. Noyes, and the UVM undergraduate students (Pamela Bay, Katherine Boucher, Dylan Devino, Michael Eldredge, Samantha Frawley, Emma Hurley, Anne Kaufman, Danielle Semick, Mallory Sullivan, Sarah Zeger) who helped with calving, sampling, and milking.This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Comparative study of methods for extraction and purification of environmental DNA from high-strength wastewater sludge

DNA extraction from wastewater sludge (COD 50000 and BOD 25000 mg/l) was conducted using nine different methods normally used for environmental samples including a procedure used in this study and the results obtained were compared. The quality of the differently extracted DNAs was subsequently assessed by measuring humic acid concentration, cell lysis efficiency, polymerase chain reaction (PCR) amplification of methanogenic and eubacterial 16S rDNA. The protocol developed in this study was further evaluated by extracting DNA from various high-strength wastewater sludge samples, denaturing gradient gel electrophoresis (DGGE) and fluorescent in situ hybridization (FISH) analyses. The results revealed that great differences existed among the nine procedures and only a few produced satisfactory results when applied to high-strength wastewater sludge. Thermal shock alone was shown inefficient to disrupt the methanogenic cell wall to release the DNA. The method presented in this study (Procedure 9) is generally recommended because of the low concentration of contaminants and its high efficiency despite its simplicity

Examination of the rumen bacteria and methanogenic archaea of wild impalas (Aepyceros melampus melampus) from Pongola, South Africa

Although the rumen microbiome of domesticated ruminants has been evaluated, few studies have explored the rumen microbiome of wild ruminants, and no studies have identified the rumen microbiome in the impala (Aepyceros melampus melampus). In the present study, next-generation sequencing and real-time polymerase chain reaction were used to investigate the diversity and density of the bacteria and methanogenic archaea residing in the rumen of five adult male impalas, culled during the winter dry season in Pongola, South Africa. A total of 15,323 bacterial 16S rRNA gene sequences (from five impala), representing 3,892 different phylotypes, were assigned to 1,902 operational taxonomic units (OTUs). A total of 20,124 methanogen 16S rRNA gene sequence reads (from four impala), of which 5,028 were unique, were assigned to 344 OTUs. From the total sequence reads, Bacteroidetes, Proteobacteria, and Firmicutes were the most abundant bacterial phyla. While the majority of the bacterial genera found were unclassified, Prevotella and Cupriavidus were the most abundant classified genera. For methanogens, the genera Methanobrevibacter and Methanosphaera represented 94.3 % and 4.0 % of the classified sequences, respectively. Most notable was the identification of Methanobrevibacter thaueri-like 16S rRNA gene sequence reads in all four impala samples, representing greater than 30 % of each individual’s total sequences. Both data sets are accessible through NCBI’s Sequence Read Archive (SRA), under study accession number SRP [048619]. The densities of bacteria (1.26×1010–3.82×1010 cells/ml whole rumen contents) and methanogens (4.48×108–7.2×109 cells/ml of whole rumen contents) from five individual impala were similar to those typically observed in domesticated ruminants.http://link.springer.com/journal/2482016-04-30hb201

A chemical survey of exoplanets with ARIEL

Thousands of exoplanets have now been discovered with a huge range of masses, sizes and orbits: from rocky Earth-like planets to large gas giants grazing the surface of their host star. However, the essential nature of these exoplanets remains largely mysterious: there is no known, discernible pattern linking the presence, size, or orbital parameters of a planet to the nature of its parent star. We have little idea whether the chemistry of a planet is linked to its formation environment, or whether the type of host star drives the physics and chemistry of the planet’s birth, and evolution. ARIEL was conceived to observe a large number (~1000) of transiting planets for statistical understanding, including gas giants, Neptunes, super-Earths and Earth-size planets around a range of host star types using transit spectroscopy in the 1.25–7.8 μm spectral range and multiple narrow-band photometry in the optical. ARIEL will focus on warm and hot planets to take advantage of their well-mixed atmospheres which should show minimal condensation and sequestration of high-Z materials compared to their colder Solar System siblings. Said warm and hot atmospheres are expected to be more representative of the planetary bulk composition. Observations of these warm/hot exoplanets, and in particular of their elemental composition (especially C, O, N, S, Si), will allow the understanding of the early stages of planetary and atmospheric formation during the nebular phase and the following few million years. ARIEL will thus provide a representative picture of the chemical nature of the exoplanets and relate this directly to the type and chemical environment of the host star. ARIEL is designed as a dedicated survey mission for combined-light spectroscopy, capable of observing a large and well-defined planet sample within its 4-year mission lifetime. Transit, eclipse and phase-curve spectroscopy methods, whereby the signal from the star and planet are differentiated using knowledge of the planetary ephemerides, allow us to measure atmospheric signals from the planet at levels of 10–100 part per million (ppm) relative to the star and, given the bright nature of targets, also allows more sophisticated techniques, such as eclipse mapping, to give a deeper insight into the nature of the atmosphere. These types of observations require a stable payload and satellite platform with broad, instantaneous wavelength coverage to detect many molecular species, probe the thermal structure, identify clouds and monitor the stellar activity. The wavelength range proposed covers all the expected major atmospheric gases from e.g. H2O, CO2, CH4 NH3, HCN, H2S through to the more exotic metallic compounds, such as TiO, VO, and condensed species. Simulations of ARIEL performance in conducting exoplanet surveys have been performed – using conservative estimates of mission performance and a full model of all significant noise sources in the measurement – using a list of potential ARIEL targets that incorporates the latest available exoplanet statistics. The conclusion at the end of the Phase A study, is that ARIEL – in line with the stated mission objectives – will be able to observe about 1000 exoplanets depending on the details of the adopted survey strategy, thus confirming the feasibility of the main science objectives.Peer reviewedFinal Published versio