1,721,094 research outputs found
Continued isolation of anaerobic gut fungi from marsupial hosts
No full textAnaerobic gut fungi (AGF) are commonly found in the digestive tracts of herbivores, where they play a crucial role in breaking down complex plant materials, such as cellulose and lignin, by adhering to plant biomass and producing enzymes and bioactive molecules that break down these complex sugars. AGF are particularly important in ruminants, such as cows and sheep, but they have also been found in other herbivorous animals, including marsupials, reptiles, and birds. The presence of AGF in marsupials, which are non-placental mammals that diverged from placental mammals approximately 125 million years ago, is strongly supported by both microscopic and sequence-based evidence. Because marsupials diverged early from other mammals and have been geographically isolated, they may represent an untapped source of undiscovered AGF genera. Previous efforts from our lab have successfully isolated two different AGF genera from captive marsupials, Eutestudomyces from a koala, and Khoyollomyces from a red kangaroo. It is of note that both AGF genera are early branching within the phylum and represent some of the oldest known representatives. We obtained fresh fecal samples from several kangaroos and wallabies in Oklahoma and are currently attempting to cultivate and identify new strains of AGF from these samples. Our approach involves utilizing a rumen fluid-based media under rigorous anaerobic conditions that has been supplemented with plant substrates and antibiotics to inhibit the growth of unwanted organisms. A successful enrichment is indicated by the visible development of bubbles and fungal biomass and increased pressure within the tube. Successive rounds of subculturing and picking colonies from roll tubes ensures the isolation of individual strains. Continuing to isolate AGF from marsupials will provide greater insight into the diversity and biology of these microorganisms and open up new possibilities for their use in various fields such as veterinary medicine, biofuels, and biomedical engineering.Biochemistry and Molecular BiologyMicrobiology and Molecular Genetic
Culturing novel anaerobic gut fungi from marsupials
No full textAnaerobic gut fungi (AGF) from the phylum Neocallimastigomycota are an essential part of the microbiome in herbivores. These fungi aid in digestion in ruminants, pseudoruminants, and nonruminants alike, where they adhere to plant biomass and produce enzymes and bioactive molecules that break down complex sugars. This includes the degradation of cellulose, which is essential in the development of biofuels and other biotechnologies converting plant biomass to products of commercial value. Marsupials, non-placental mammals who split from placental mammals ~125 Mya, have shown strong microscopic and sequence-based evidence for harboring AGF. Marsupial herbivores are promising hosts for uncovering novel AGF because some species are foregut fermenters (kangaroos and wallabies) and others are hindgut fermenters (koalas and wombats), both digestive methods that are associated with AGF presence in other herbivores. Due to their laborious maintenance procedures, strict anaerobic nature, and technical difficulties in genomic sequencing, these microorganisms are under-researched and poorly sampled.We hypothesized that marsupials represent a yet-untapped reservoir for discovering novel AGF taxa. To test this hypothesis, we collected fresh fecal samples from a wide range of marsupials and are currently attempting to enrich and isolate novel AGF taxa from these samples. Using complex media amended with plant substrates, strict anaerobic techniques, and multiple antibiotics for suppressing growth, we were able to enrich for AGF, as evident by visual production of hyphal filaments in enrichment tubes. We are currently undertaking purification procedures to isolate axenic cultures of AGF for subsequent identification and characterization. Culturing novel AGF from marsupials will allow for deeper perspectives on the diversity and biology of anaerobic gut fungi and will enable their applications in veterinary medicine, biofuels, and biomedical engineering.Biochemistry and Molecular BiologyMicrobiology and Molecular Genetic
Discovery and characterization of novel fungal diversity in the equine alimentary tract
No full textFungi provide crucial ecosystem services in multiple ecosystems. Most fungi thrive as free-living organisms, but many forge symbiotic, predatory, pathogenic, and commensal relationships with algae, plants, and animals. One of the most peculiar groups of fungi are the anaerobic gut fungi (phylum Neocallimastigomycota) that reside in the alimentary tract of herbivores. Little is known regarding the scope of diversity of these elusive, anoxic microorganisms. Our work aims to characterize the diversity of AF’s in the herbivorous gut on a global scale using culture independent approaches. We have collected >1,000 samples, from >50 type of animals, across 5 continents. My focus in this broader project is to examine patterns and determinants of the diversity of AF in equine alimentary tract. To this end, I extracted DNA from >100 fecal horse samples, and used polymerase chain reaction (PCR) to amplify a specific marker gene (D1/D2 LSU). High throughput sequencing was conducted, and analysis of the sequence data is currently underway. My preliminary analysis revealed a high level of AF diversity within the equine alimentary tract, as evident by the detection of > 30 different cultured and yet-uncultured AF genera in these samples. Moreover, a fraction of the sequenced obtained belong to multiple novel, hitherto undiscovered lineages, clearly indicated that the scope of AF diversity in the equine alimentary tract is much broader than previously suggested. Currently, I am attempting to identify and quantify the impact of various factors (animal feed, age, sex, location) in shaping the AF community in horses via implementing a wide range of statistical and phylogenetic approaches.Oklahoma Louis Stokes Alliance for Minority Participation ProgramNational Science Foundation (U.S.)Ronald E. McNair Post-Baccalaureate Achievement ProgramLew Wentz FoundationMicrobiology and Molecular Genetic
Transcriptional studies on stress-induced meiosis in the anaerobic gut fungi Pecoramyces ruminantium strain Hef-5
No full textThis study focused on the presence of a cryptic sexual life cycle of Pecoramyces ruminantium strain Hef-5. This strain of anaerobic gut fungi (AGF) can be found in the rumen of herbivorous animals and is known to enhance plant biomass metabolism via fermentation and saccharation. In all past research, this fungus has been described as strictly asexual; however, this research has been conducted based on the behavior of the organism in its natural habitat. Many other fungal organisms have been described to exhibit cryptic sexual life cycles which may only appear while the organism is under some stress. The presence of a cryptic sexual cycle can be sensed by the expression of core meiotic genes (CMGs). The three CMGs studied are Hop2, required for homologous pairing, Mnd1, required for recombination and nuclear division, and Dmc1, required for dsDNA break repair and homologous pairing. To impart stress on the organism, samples were flushed with oxygen for increasing increments of five minutes up to one hour, two samples for each time frame. The expression of Hop2 came first at the 10-minute mark and continues to be expressed with few discrepancies through the 60 minute time frame. Dmc1 expression begins at the 20-minute mark and stays, also with few discrepancies, through until the 55-minute mark. Mnd1 is the final CMG to be expressed after 25 minutes of oxygen exposure and continues to be expressed through the 60-minute trial. These results indicate that the AGF strain Hef-5 could have a cryptic sexual cycle under these conditions. The negative control showed no expression for any of the three CMGs, supporting the hypothesis. The continuous expression of these CMGs aligns well with the time frame for meiosis I is S. cerevisiae. Future research to expand this includes a full transcriptomic study of Hef-5 as well as the study of additional CMGs involved in other phases of meiosis
BTEX Degradation at High Salinity in Rozel Point
No full textRozel Point is a unique habitat since it is highly saline and also contaminated with high levels crude oil from natural seeps. Unfortunately, very few studies were carried out to understand microbial diversity and their capacity to degrade petroleum compounds at Rozel Point. While halophiles have been shown to degrade aliphatic, aromatic, and poly aromatic compounds, little is known about the fate of benzene, toluene, ethylbenzene, and xylenes (BTEX) in saline environments. Therefore, our study explores bacterial degradation of BTEX in Rozel Point sediment. We obtained a highly enriched microbial consortium from a sediment sample from Rozel Point and assessed its BTEX degradation ability at various salt concentrations. We also identified the microbial community composition of the enrichment and determined major pathway of benzene metabolism using cloning and sequencing techniques. These studies are important for understanding natural attenuation potential of hydrocarbons at Rozel Point and also for designing in-situ bioremediation techniques for contaminated saline habitats.nThe enrichment degraded benzene and toluene across a wide rang of salinities including 0 to 5 M NaCl. Very few studies have shown such ability, though many contaminated habitats are hypersaline. Our studies have shown that benzene and toluene are primarily degraded via catechol and meta-cleavage pathway. Molecular analysis of microbial community composition of the enrichment revealed that the Gammaproteobacter and Bacteriodetes formed the dominant groups. We also successfully isolated a pure culture that degrades benzene or toluene as the sole source of carbon. Phylogenetic analysis shows that the isolate's 16S rRNA-gene sequence had only 93% sequence identity to Arhodomonas aquaeolei suggesting that perhaps the isolate is a novel species in the Gammaproteobacteri. The organism degrades benzene in the presence of 1 to 4 M NaCl with an optimal degradation at 3 M salt. Also, the isolate degrades benzene in the presence of easily utilizable substrates including glucose, pyruvate, or acetate. This is important since most contaminated sites also contain a variety of organic compounds and inhibition of degradation often occurs in the presence of easily utilizable substrates. In conclusion, very few pure cultures capable of degrading BTEX at high salinities have been isolated. Isolation of pure cultures is important for clear understanding of ecology, physiology, mechanism of degradation and how to enhance biodegradation of hydrocarbons.Department of Biochemistry and Molecular Biolog
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
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