828 research outputs found
North American Beaver (Castor canadensis) gut mycobiome
No full textThe North American Beaver (Castor canadensis) is a semi-aquatic, hindgut-fermenting rodent that follows a tree bark-based diet and shows long feed retention time (14-40 hours). Their enlarged cecum harbors a complex microbial community that plays a key role in lignocellulose degradation. While some studies have investigated its gut microbiome, most focused on bacteria and archaea with little attention to the fungal community. Since anaerobic gut fungi (AGF) are known lignocellulose degraders in other herbivores, we hypothesize that beavers host AGF and furthermore possess a unique fungal community due to their lignocellulose-rich diet.
To test this hypothesis, cecal samples from 32 wild beavers were collected by trappers throughout the state of Utah. Amplicon sequencing targeting the D2 region of the LSU rRNA gene of the general fungal community has been performed. Preliminary results showed that Neocallimastigomycota constituted an integral component of the beaver’s gut (~23% of the total fungal community). Within this AGF community, genera encountered included Orpinomyces, Liebetanzomyces, and a novel genus in the Joblinomyces clade. Other than Neocallimastigomycota, the beaver gut harbored novel fungal lineages closely related to the Neocallimastigomycota and Chytridiomycota (~63% of the total fungal community). Comparative analysis of all 32 samples will elucidate community differences based on sex, age, and weight. In addition, enrichment and isolation efforts are underway.
This study provides the first report of AGF in beavers and aims to comprehensively characterize the fungal community associated with North American beavers.Microbiology and Molecular Genetic
Assessing the anaerobic gut fungal diversity in herbivores using culture-independent survey and multi-year isolation
No full textThe overall aim of my dissertation was to investigate the phylogenetic diversity, ecological distribution, and community structure of the anaerobic gut fungi (Neocallimastigomycota) in a wide range of herbivorous animals with special emphasis on hitherto unsampled herbivores. To achieve this aim, two approaches were employed in parallel, anaerobic culturing approaches as well as a culture-independent diversity survey. I conducted a multi-year isolation effort utilizing different isolation techniques, which maximized the recovery of multiple AGF isolates. My strategy involved the utilization of multiple carbon sources for AGF enrichment, sequence-guided strategy to target samples enriched in uncultured taxa, and sampling from a wide range of wild, domesticated, and zoo-housed herbivorous animals. This effort has resulted in the characterization of 10 novel AGF genera including five multiple previously uncultured AGF members. This resulted in more than doubling of the number of AGF genera with a cultured representative. This extensive culturing-based study was complemented with a culture-independent survey to evaluate AGF diversity in 27 herbivorous animals. The culture-independent survey also served to evaluate the utility of the D1/D2 region of the LSU rRNA as a new phylomarker for the AGF. The analysis produced the first comprehensive reference D1/D2 LSU database encompassing all cultured AGF genera, as well as the majority of candidate genera previously only identified in prior ITS1-based culture-independent surveys. Using the created database, I was able to identify a highly diverse anaerobic fungal community within the sampled animals, with twenty-eight genera and candidate genera, including multiple novel lineages. This work has established a framework for future utilization of D1/D2 LSU amplification and PacBio sequencing for AGF community assessment, and highlight the value of wild herbivores as untapped reservoirs for many yet-uncultured AGF taxa. Collectively, the results from this dissertation show that the genus-level diversity within Neocallimastigomycota is significantly broader than what was previously proposed, and argue that a large number of the yet-uncultured AGF genera are indeed culturable, given the right sampling and isolation conditions
Leveraging -omics based approaches to explore environments: A look at two domains of life
No full textRapid advancements in technology have both dramatically lowered the cost of sequencing as well as increased the depth of information gleaned. With such a low barrier of entry, increasing numbers of scientists around the globe are generating unprecedented amounts of data pertaining to the identity and function of the various microbes that impact assorted environments, from within a host to various biomes in nature. Understandably, a pressing challenge in the field centers on how to process and interpret these large quantities of precise information. The leveraging of -omics based techniques used in bioinformatics stands poised to answer this challenge, enabling discoveries that probe not just what a microbe can do, but also perhaps provide a look into their past through an analysis of their genetic potential.For my overall project, I sought to leverage various -omics based approaches to study how various organisms impact and have been impacted by their respective environments. My work has spread from transcriptomics to proteomics and finally metagenomics, from pure cultures to environmental samples, and from fungi to bacteria. At the surface levels, these works provide a form of functional profile of the studied organisms; however, deeper insights into the potential evolutionary history can also be made. For example, the study on the anaerobic gut fungal phylum Neocallimastigomycota (Chapter I) can provide insights into the clade's intertwined history with the development of herbivory, the study on the obligate plant symbiont Rhizophagus irregularis (Chapter II) can provide insight into fungal association with plants, the metagenomic studies of the Binatota (Chapter III) and novel Desulfobacterota classes (Chapter IV) can provide insights into the development and evolution of the Delta Proteobacteria into a diverse clade, and the study of novel Myxococcota classes (Chapter V) can provide clues into the development of predation strategies in bacteria. As a whole, this body of works provides a jumping-off point for future probes into these organisms, as well as potential isolation strategies for the uncultured organisms discussed
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
Cataglyphis laylae Cedric A. Collingwood & Donat Agosti & Mostafa R. Sharaf & Antonius van Harten 2011, nov. spec.
No full textCataglyphis laylae Collingwood nov. spec. Plates 96–103 Cataglyphis desertorum Forel, 1894, teste Collingwood, 1985; unavailable name according to Agosti (1990). Specimens examined: Holotype: 1 ☿, United Arab Emirates, al-Ain [24°13'N 55°46'E], iii.1995, leg. C.A. Collingwood (MHNG). Paratypes: 3 ☿, al-Ain zoo, 13.iii.2005, CAC. 1 ☿, Remah, 9.iii.1995, CCA. 3 ☿, Remah, resthouse, 250 m, irrigated sand dune [24°10'37"N 55°18'6"E], 18.iii.1995, leg. D. Agosti. 6 ☿, Remah, resthouse, 250 m, irrigated sand dune, nest with one entrance, [24°10'37"N, 55°18'6"E], 18.iii.1995, leg. D. Agosti. 1 ☿, Sharjah Desert Park, 5–6.x.2004, AvH; 1 ☿, 3.iii.2005, CAC. 1 ☿, al- Za'aba, 100 m, sandy soil with Rhaisa stricta [23°43'20"N, 55°33'49"E], 22.iii.1995, leg. D. Agosti. Description: A large worker from al-Ain was selected as holotype. The measurements are as follows: total length 8.40; head width 3.60; head length 4.20; scape length 3.84; funicular segment I 0.40; funicular segment II 0.23; petiole length 1.10; petiole width 0.72. Colour dark reddish brown. There are no exterior hairs on the scapes or hind tibia. The gaster, petiole and propodeum have dorsal hairs. Remarks: This species thought to correspond with C. desertorum has to be described as a new species. In fact it is one of the commonest Cataglyphis in southern Arabia. The main distinguishing feature compared with other dark Cataglyphis is the slender petiole, which has the anterior face more sloped than in other similar species such as C. niger (André, 1882) and C. savignyi (Dufour, 1862). Biology: Cataglyphus laylae nov. spec. does not appear to occur in open sandy desert and is most abundant in disturbed habitats such as man-developed plantations and open cultivated fields. Distribution: This species was recorded by Collingwood (1985) as C. desertorum from Saudi Arabia and Oman and as Cataglyphis spec. by Collingwood & Agosti (1996). Etymology: The new species is named after a village settlement called “Layla”, just north of Riyadh (Saudi Arabia) in the area where the author (CAC) first encountered it in numbers in an Acacia plantation.Published as part of Cedric A. Collingwood, Donat Agosti, Mostafa R. Sharaf & Antonius van Harten, 2011, Order Hymenoptera, family Formicidae, pp. 1-70 in Arthropod fauna of the UAE 4 on page 54, DOI: 10.5281/zenodo.116858
A Sustainable Two-Echelon Logistics Model with Shipment Consolidation
No full textBackground: Shipment consolidation is a concept in logistics management in which two or more shipments are transported by using the same vehicle with the aim of using less resources. Methods: The objective of this manuscript is to study shipment consolidation and assess its impact on cost environment, to achieve this, a mathematical model was developed to optimize shipment consolidation while reducing the emissions and minimizing the costs. Results: A case study from major dairy products manufacturers in Egypt was used to validate the model and evaluate the outcomes. A comparison was made between two transportation models, with and without consolidation. Results show that shipment consolidation reduced the total costs by 40% in addition to consuming less fuel, and consequently producing less emissions. Conclusions: These findings emphasize the importance of shipment consolidation and how it can be used to achieve more sustainability in logistics management
L’année de Bacchus d’El Mostafa Bouignane entre devoir de la mémoire et exaltation de la vie
No full textThis study will discuss the approach to the structure and narrative composition of the novel entitled L\u27année de Bacchus by Mostafa Bouignane, published by Virgule Editions in 2020. This text adds to a series of stories of which Bouignane constructs a narrative universe to reveal the nature of man who, even submissive and reduced, remains capable of regaining his freedom and leading a peaceful life. Thus, our study will propose an analysis of the ideological and historical dimension of this text representative of the literary experience of the author, then at the end the questioning of his human and moral values
Exploring environmental adaptations and habitat preferences in three microbial lineages using comparative (meta)genomic approaches
No full textThe utilization of -omics based approaches (metagenomics, genomics, transcriptomics, proteomics, and metabolomics) in the field of microbiology has greatly advanced our understanding of the microbial world. The utilization of such approaches, either on pure cultures, or directly on environmental samples has provided novel insights into the role of microorganisms in earth biogeochemical cycles, microbial evolutionary dynamics, and their potential biotechnological applications. In the field of microbial pathogenesis, informatics-based methods have helped in uncovering several venues of pathogenesis including pathogens strain-specific characteristics, virulence genes, antimicrobial resistance, and understanding the landscape of various diseases.Here, I present my 3 research projects based on exploiting various -omics based approaches to understand the ecology, evolution, and pathogenic determinants of various groups of cultured, and yet- uncultured microorganisms. In chapter I, I implemented genome-resolved metagenomics to elucidate the ecological roles, metabolic capabilities, and physiological preferences of a novel yet-uncultured microbial phylum recovered from enrichments of tertiary oil reservoir. I showed that this lineage is a slow-growing member of rare biosphere and an aminolytic halothermophilic organism. We proposed creating a new candidate phylum "Mcinerneybacteriota" to accommodate this organism. This work has been published in the journal “Systematic and Applied Microbiology”. In chapter II, I analyzed multiple genome-resolved metagenomes of uncultured Group 18 Acidobacteria to understand their biogeochemical roles and elucidate the key evolutionary innovations that enable Acidobacteria to thrive in soil ecosystems. I demonstrated that soil-dwelling genera were characterized by larger genomes, higher CRISPR loci, expanded CAZyme machinery, possession of a C1 metabolism, and a sole dependence on aerobic respiration, whereas nonsoil genomes encoded a more versatile respiratory capacity and potential for utilizing the Wood-Ljungdahl (WL) pathway as an electron sink. This work is published in the journal “Applied and Environmental Microbiology”. Lastly, my third project (Chapter III) is about utilizing genomics and transcriptomics for an intracellular pathogen, Coxiella burnetii, to understand the changes in its genes crucial for intracellular success during long-term culturing in an axenic media. Here, I showed the expression changes and mutations in multiple genes that are known or most likely predicted to be crucial to their normal intracellular growth lifestyle or pathogenesis
Microbiome-based approaches to mitigate coccidiosis and necrotic enteritis in chickens
No full textCoccidiosis and necrotic enteritis (NE), caused by Eimeria and Clostridium perfringens respectively, are two most economically significant poultry diseases managed traditionally by antibiotics. However, a rise in antibiotic resistance has led to a ban of in-feed antibiotics in livestock and poultry production in a growing number of countries. Consequently, alternative strategies to mitigate coccidiosis and NE are urgently needed. Manipulating the intestinal microbiome presents a promising approach. This dissertation encompasses three studies aimed at investigating the intestinal microbiota alterations in broiler chickens in response to coccidiosis and NE and further evaluating the feasibility of microbiota transplantation for NE mitigation.
In the first study, we examined the dynamic changes in both the ileal and cecal intestinal microbiomes following Eimeria maxima infection over a 14-day period. E. maxima infection was found to trigger intestinal dysbiosis coinciding with the Eimeria life cycle. Minimal changes in the gut microbiota were observed during early infection (0-3 days post-infection, dpi), whereas significant alterations occurred during acute infection (5-7 dpi). Upon recovery (10-14 dpi), the gut microbiota tended to revert to a healthy state. Major short-chain fatty acid-producing bacteria, such as Faecalibacterium, were suppressed by E. maxima in the cecum. Opportunistic pathogens, such as Escherichia, were significantly enriched in the ileum during acute infection.
The second study aimed to elucidate the individual impacts of E. maxima and C. perfringens on NE-mediated alterations in intestinal microbiota composition and function. Our findings indicate that the substantial changes in the intestinal microbiota of NE-infected chickens result from the combined effects of both E. maxima and C. perfringens, with E. maxima playing a more pronounced role. Moreover, NE infection significantly enriched bacterial genes involved in C. perfringens toxin production, biofilm formation, and lipopolysaccharide biosynthesis. Notably, evident intestinal dysbiosis was observed at 5 days post-infection (dpi) with E. maxima, while more severe dysbiosis occurred in chickens co-infected with both E. maxima and C. perfringens, with the most drastic changes observed at 3 dpi.
In the third study, we compared the intestinal microbiota of two highly inbred chicken lines, Fayoumi M5.1 (FM5.1) and Leghorn line Ghs6, as well as Cobb broiler chickens, under both healthy and NE conditions. A significant number of differentially enriched bacterial taxa were identified. We also investigated the efficacy of cecal microbiota transplantation (CMT) from FM5.1, Ghs6, and Cobb chickens in protecting newly hatched Cobb chickens from experimental NE. The results revealed that the cecal microbiota from FM5.1 chickens provided the most protection against NE.
Collectively, these findings will provide important leads for the development of novel microbiota-based diagnostic or therapeutic approaches for the control and prevention of coccidiosis and NE in poultry
Using Lean Tools in Warehouse Improvement: A Case Study from Electronics Retail Sector
No full textThe purpose of this study is to investigate the use of lean tools in the improvement of warehouses in terms of reducing costs and waste in a warehouse. After the determination of waste, specific lean tools were used to reduce waste and improve the performance of the warehouse. To evaluate the warehouse efficiency, value stream mapping, benchmarking, and activity profiling were used. The combination of these three tools facilitates the identification of waste in the warehouse that would have been challenging to identify using only one tool. As a solution to reduce lead time and non-value-added activities in the warehouse, various lean tools including 5S and visual management were implemented. The main critical issue in applying lean is to sustain the work and to sustain the idea of continuous improvement, hence employees’ training was key in improvement. A future state map was conducted after applying lean tools, it was concluded that the lead time has decreased by 25%, and non-value-added activities time was reduced by 33% in various operations such as loading, receiving, storage, inspection, and order picking
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