scholarly journals Comparative genome analysis of Clostridium beijerinckii strains isolated from pit mud of Chinese strong flavor baijiu ecosystem

2021 ◽  
Author(s):  
Wei Zou ◽  
Guangbin Ye ◽  
Chaojie Liu ◽  
Kaizheng Zhang ◽  
Hehe Li ◽  
...  
Keyword(s):  
Core Genome ◽  
Carbon Sources ◽  
Clostridium Beijerinckii ◽  
Orthologous Genes ◽  
The Core ◽  
Phage Integrase ◽  
Pit Mud ◽  
Wide Range ◽  
Current Sampling ◽  
Acetate Butyrate

Abstract Clostridium beijerinckii is a well-known anaerobic solventogenic bacterium which inhabits a wide range of different niches. Previously, we isolated five butyrate-producing C. beijerinckii strains from pit mud (PM) of strong-flavor baijiu (SFB) ecosystems. Genome annotation of the five strains showed that they could assimilate various carbon sources as well as ammonium to produce acetate, butyrate, lactate, hydrogen, and esters but did not produce the undesirable flavours isopropanol and acetone, making them useful for further exploration in SFB production. Our analysis of the genomes of an additional 233 C. beijerinckii strains revealed an open pangenome based on current sampling and will likely change with additional genomes. The core genome, accessory genome, and strain-specific genes comprised 1567, 8851, and 2154 genes, respectively. A total of 298 genes were found only in the five C. beijerinckii strains from PM, among which only 77 genes were assigned to Clusters of Orthologous Genes (COG) categories. In addition, 15 transposase and 12 phage integrase families were found in all five C. beijerinckii strains from PM. Between 18 and 21 genome islands (GIs) were predicted for the five C. beijerinckii genomes. The existence of a large number of MGEs indicated that the genomes of the five C. beijerinckii strains evolved with the loss or insertion of DNA fragments in the PM of SFB ecosystems. This study presents a genomic framework of C. beijerinckii strains from PM that could be used for genetic diversification studies and further exploration of these strains.

scholarly journals Diversity and Evolution of Clostridium beijerinckii and Complete Genome of the Type Strain DSM 791T

Processes ◽  
2021 ◽  
Vol 9 (7) ◽  
pp. 1196
Author(s):  
Karel Sedlar ◽  
Marketa Nykrynova ◽  
Matej Bezdicek ◽  
Barbora Branska ◽  
Martina Lengerova ◽  
...  
Keyword(s):  
Complete Genome ◽  
Functional Annotation ◽  
Type Strain ◽  
Core Genome ◽  
Clostridium Beijerinckii ◽  
High Quality ◽  
Circular Chromosome ◽  
The Core ◽  
Different Strains ◽  
Genome Assemblies

Clostridium beijerinckii is a relatively widely studied, yet non-model, bacterium. While 246 genome assemblies of its various strains are available currently, the diversity of the whole species has not been studied, and it has only been analyzed in part for a missing genome of the type strain. Here, we sequenced and assembled the complete genome of the type strain Clostridium beijerinckii DSM 791T, composed of a circular chromosome and a circular megaplasmid, and used it for a comparison with other genomes to evaluate diversity and capture the evolution of the whole species. We found that strains WB53 and HUN142 were misidentified and did not belong to the Clostridium beijerinckii species. Additionally, we filtered possibly misassembled genomes, and we used the remaining 237 high-quality genomes to define the pangenome of the whole species. By its functional annotation, we showed that the core genome contains genes responsible for basic metabolism, while the accessory genome has genes affecting final phenotype that may vary among different strains. We used the core genome to reconstruct the phylogeny of the species and showed its great diversity, which complicates the identification of particular strains, yet hides possibilities to reveal hitherto unreported phenotypic features and processes utilizable in biotechnology.

scholarly journals Exploration of Survival Traits, Probiotic Determinants, Host Interactions, and Functional Evolution of Bifidobacterial Genomes Using Comparative Genomics

Genes ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 477 ◽  
Author(s):  
Vikas Sharma ◽  
Fauzul Mobeen ◽  
Tulika Prakash
Keyword(s):  
Core Genome ◽  
Size Variation ◽  
Genomic Islands ◽  
Genome Size Variation ◽  
Host Interactions ◽  
The Core ◽  
Pan Genome ◽  
Wide Range ◽  
Insertion Elements ◽  
Open Nature

Members of the genus Bifidobacterium are found in a wide-range of habitats and are used as important probiotics. Thus, exploration of their functional traits at the genus level is of utmost significance. Besides, this genus has been demonstrated to exhibit an open pan-genome based on the limited number of genomes used in earlier studies. However, the number of genomes is a crucial factor for pan-genome calculations. We have analyzed the pan-genome of a comparatively larger dataset of 215 members of the genus Bifidobacterium belonging to different habitats, which revealed an open nature. The pan-genome for the 56 probiotic and human-gut strains of this genus, was also found to be open. The accessory- and unique-components of this pan-genome were found to be under the operation of Darwinian selection pressure. Further, their genome-size variation was predicted to be attributed to the abundance of certain functions carried by genomic islands, which are facilitated by insertion elements and prophages. In silico functional and host-microbe interaction analyses of their core-genome revealed significant genomic factors for niche-specific adaptations and probiotic traits. The core survival traits include stress tolerance, biofilm formation, nutrient transport, and Sec-secretion system, whereas the core probiotic traits are imparted by the factors involved in carbohydrate- and protein-metabolism and host-immunomodulations.

Duoethnography: A Polytheoretical Approach to (Re)Storing, (Re)Storying the Meanings That One Gives

2020 ◽  
pp. 396-423
Author(s):  
John Joseph Norris ◽  
Richard D. Sawyer
Keyword(s):  
Social Justice ◽  
Critical Theory ◽  
Third Space ◽  
The Third ◽  
The Core ◽  
Wide Range ◽  
Core Elements ◽  
Feminist Inquiry

This chapter summarizes the advancement of duoethnography throughout its fifteen-year history, employing examples from a variety of topics in education and social justice to provide a wide range of approaches that one may take when conducting a duoethnography. A checklist articulates what its cofounders consider the core elements of duoethnographies, additional features that may or may not be employed and how some studies purporting to be duoethnographies may not be so. The chapter indicates connections between duoethnography and a number of methodological concepts including the third space, the problematics of representation, feminist inquiry, and critical theory using published examples by several duoethnographers.

scholarly journals Burkholderia thailandensis E264 as a promising safe rhamnolipids’ producer towards a sustainable valorization of grape marcs and olive mill pomace

2021 ◽  
Author(s):  
Alif Chebbi ◽  
Massimiliano Tazzari ◽  
Cristiana Rizzi ◽  
Franco Hernan Gomez Tovar ◽  
Sara Villa ◽  
...  
Keyword(s):  
Energy Source ◽  
Olive Oil ◽  
Low Cost ◽  
Carbon Sources ◽  
Burkholderia Thailandensis ◽  
Rhamnolipid Production ◽  
Key Points ◽  
Wide Range ◽  
Long Chain ◽  
Olive Mill

Abstract Within the circular economy framework, our study aims to assess the rhamnolipid production from winery and olive oil residues as low-cost carbon sources by nonpathogenic strains. After evaluating various agricultural residues from those two sectors, Burkholderia thailandensis E264 was found to use the raw soluble fraction of nonfermented (white) grape marcs (NF), as the sole carbon and energy source, and simultaneously, reducing the surface tension to around 35 mN/m. Interestingly, this strain showed a rhamnolipid production up to 1070 mg/L (13.37 mg/g of NF), with a higher purity, on those grape marcs, predominately Rha-Rha C14-C14, in MSM medium. On olive oil residues, the rhamnolipid yield of using olive mill pomace (OMP) at 2% (w/v) was around 300 mg/L (15 mg/g of OMP) with a similar CMC of 500 mg/L. To the best of our knowledge, our study indicated for the first time that a nonpathogenic bacterium is able to produce long-chain rhamnolipids in MSM medium supplemented with winery residues, as sole carbon and energy source. Key points • Winery and olive oil residues are used for producing long-chain rhamnolipids (RLs). • Both higher RL yields and purity were obtained on nonfermented grape marcs as substrates. • Long-chain RLs revealed stabilities over a wide range of pH, temperatures, and salinities

scholarly journals Sporulation in solventogenic and acetogenic clostridia

2021 ◽  
Author(s):  
Mamou Diallo ◽  
Servé W. M. Kengen ◽  
Ana M. López-Contreras
Keyword(s):  
Current Knowledge ◽  
Carbon Sources ◽  
Cost Effective ◽  
Biotechnological Production ◽  
Key Points ◽  
Wide Range ◽  
Potential Applications ◽  
A Cell ◽  
Sporulation Initiation ◽  
Solventogenic Clostridia

AbstractThe Clostridium genus harbors compelling organisms for biotechnological production processes; while acetogenic clostridia can fix C1-compounds to produce acetate and ethanol, solventogenic clostridia can utilize a wide range of carbon sources to produce commercially valuable carboxylic acids, alcohols, and ketones by fermentation. Despite their potential, the conversion by these bacteria of carbohydrates or C1 compounds to alcohols is not cost-effective enough to result in economically viable processes. Engineering solventogenic clostridia by impairing sporulation is one of the investigated approaches to improve solvent productivity. Sporulation is a cell differentiation process triggered in bacteria in response to exposure to environmental stressors. The generated spores are metabolically inactive but resistant to harsh conditions (UV, chemicals, heat, oxygen). In Firmicutes, sporulation has been mainly studied in bacilli and pathogenic clostridia, and our knowledge of sporulation in solvent-producing or acetogenic clostridia is limited. Still, sporulation is an integral part of the cellular physiology of clostridia; thus, understanding the regulation of sporulation and its connection to solvent production may give clues to improve the performance of solventogenic clostridia. This review aims to provide an overview of the triggers, characteristics, and regulatory mechanism of sporulation in solventogenic clostridia. Those are further compared to the current knowledge on sporulation in the industrially relevant acetogenic clostridia. Finally, the potential applications of spores for process improvement are discussed.Key Points• The regulatory network governing sporulation initiation varies in solventogenic clostridia.• Media composition and cell density are the main triggers of sporulation.• Spores can be used to improve the fermentation process.

Measurements and Modeling of Ingress in a New 1.5-Stage Turbine Research Facility

2016 ◽  
Vol 139 (1) ◽  
Author(s):  
Marios Patinios ◽  
James A. Scobie ◽  
Carl M. Sangan ◽  
J. Michael Owen ◽  
Gary D. Lock
Keyword(s):  
Theoretical Model ◽  
Gas Turbines ◽  
Test Facility ◽  
Radial Clearance ◽  
Operating Life ◽  
The Core ◽  
Wide Range ◽  
Purge Flow ◽  
Rotor Disk ◽  
Engine Components

In gas turbines, hot mainstream flow can be ingested into the wheel-space formed between stator and rotor disks as a result of the circumferential pressure asymmetry in the annulus; this ingress can significantly affect the operating life, performance, and integrity of highly stressed, vulnerable engine components. Rim seals, fitted at the periphery of the disks, are used to minimize ingress and therefore reduce the amount of purge flow required to seal the wheel-space and cool the disks. This paper presents experimental results from a new 1.5-stage test facility designed to investigate ingress into the wheel-spaces upstream and downstream of a rotor disk. The fluid-dynamically scaled rig operates at incompressible flow conditions, far removed from the harsh environment of the engine which is not conducive to experimental measurements. The test facility features interchangeable rim-seal components, offering significant flexibility and expediency in terms of data collection over a wide range of sealing flow rates. The rig was specifically designed to enable an efficient method of ranking and quantifying the performance of generic and engine-specific seal geometries. The radial variation of CO2 gas concentration, pressure, and swirl is measured to explore, for the first time, the flow structure in both the upstream and downstream wheel-spaces. The measurements show that the concentration in the core is equal to that on the stator walls and that both distributions are virtually invariant with radius. These measurements confirm that mixing between ingress and egress is essentially complete immediately after the ingested fluid enters the wheel-space and that the fluid from the boundary layer on the stator is the source of that in the core. The swirl in the core is shown to determine the radial distribution of pressure in the wheel-space. The performance of a double radial-clearance seal is evaluated in terms of the variation of effectiveness with sealing flow rate for both the upstream and the downstream wheel-spaces and is found to be independent of rotational Reynolds number. A simple theoretical orifice model was fitted to the experimental data showing good agreement between theory and experiment for all cases. This observation is of great significance as it demonstrates that the theoretical model can accurately predict ingress even when it is driven by the complex unsteady pressure field in the annulus upstream and downstream of the rotor. The combination of the theoretical model and the new test rig with its flexibility and capability for detailed measurements provides a powerful tool for the engine rim-seal designer.

The vulnerability of Arctic shelf sediments to climate change

2015 ◽  
Vol 23 (4) ◽  
pp. 461-479 ◽  
Author(s):  
Robie W. Macdonald ◽  
Zou Zou A. Kuzyk ◽  
Sophia C. Johannessen
Keyword(s):  
Organic Carbon ◽  
Carbon Sources ◽  
The Arctic ◽  
Sedimentary Environments ◽  
Carbon Supply ◽  
Shelf Sediment ◽  
Wide Range ◽  
Metabolic Conditions ◽  
Shelf Sediments ◽  
Ocean Ecosystem

The sediments of the pan-Arctic shelves contribute an important component to the Arctic Ocean ecosystem by providing a habitat for biota (benthos), a repository for organic and inorganic non-conservative substances entering or produced within the ocean, a reactor and source of transformed substances back to the water column, and a mechanism of burial. Sediments interact with ice, ocean, and the surrounding land over a wide range of space and time scales. We discuss the vulnerability of shelf sediment to changes in (i) organic carbon sources, (ii) pathways of sediment and organic carbon supply, and (iii) physical and biogeochemical alteration (diagenesis). Sedimentary environments of the shelves and basins are likely to exhibit a wide variance in their response to global change because of their wide variation in sediment sources, processes, and metabolic conditions. In particular, the Chukchi and Barents shelves are dominated by inflowing waters from oceans to the south, whereas the interior shelves are more closely tied to terrigenous sources due to river inflow and coastal erosion.

scholarly journals A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera

2008 ◽  
Vol 191 (1) ◽  
pp. 91-99 ◽  
Author(s):  
Marc Deloger ◽  
Meriem El Karoui ◽  
Marie-Agnès Petit
Keyword(s):  
Dna Sequences ◽  
Dna Content ◽  
Core Genome ◽  
Biological Diversity ◽  
Bacterial Species ◽  
Genomic Distance ◽  
The Core ◽  
Intraspecies Diversity ◽  
Genome Level ◽  
Definition Of

ABSTRACT The fundamental unit of biological diversity is the species. However, a remarkable extent of intraspecies diversity in bacteria was discovered by genome sequencing, and it reveals the need to develop clear criteria to group strains within a species. Two main types of analyses used to quantify intraspecies variation at the genome level are the average nucleotide identity (ANI), which detects the DNA conservation of the core genome, and the DNA content, which calculates the proportion of DNA shared by two genomes. Both estimates are based on BLAST alignments for the definition of DNA sequences common to the genome pair. Interestingly, however, results using these methods on intraspecies pairs are not well correlated. This prompted us to develop a genomic-distance index taking into account both criteria of diversity, which are based on DNA maximal unique matches (MUM) shared by two genomes. The values, called MUMi, for MUM index, correlate better with the ANI than with the DNA content. Moreover, the MUMi groups strains in a way that is congruent with routinely used multilocus sequence-typing trees, as well as with ANI-based trees. We used the MUMi to determine the relatedness of all available genome pairs at the species and genus levels. Our analysis reveals a certain consistency in the current notion of bacterial species, in that the bulk of intraspecies and intragenus values are clearly separable. It also confirms that some species are much more diverse than most. As the MUMi is fast to calculate, it offers the possibility of measuring genome distances on the whole database of available genomes.

scholarly journals From Residues to Added-Value Bacterial Biopolymers as Nanomaterials for Biomedical Applications

Nanomaterials ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1492
Author(s):  
Francisco G. Blanco ◽  
Natalia Hernández ◽  
Virginia Rivero-Buceta ◽  
Beatriz Maestro ◽  
Jesús M. Sanz ◽  
...  
Keyword(s):  
Biomedical Applications ◽  
Carbon Sources ◽  
Structural Diversity ◽  
Added Value ◽  
Nanoscale Systems ◽  
Chemical Structures ◽  
Wide Range ◽  
Peptide Functionalization ◽  
Metabolic Strategies ◽  
Drug Nanocarriers

Bacterial biopolymers are naturally occurring materials comprising a wide range of molecules with diverse chemical structures that can be produced from renewable sources following the principles of the circular economy. Over the last decades, they have gained substantial interest in the biomedical field as drug nanocarriers, implantable material coatings, and tissue-regeneration scaffolds or membranes due to their inherent biocompatibility, biodegradability into nonhazardous disintegration products, and their mechanical properties, which are similar to those of human tissues. The present review focuses upon three technologically advanced bacterial biopolymers, namely, bacterial cellulose (BC), polyhydroxyalkanoates (PHA), and γ-polyglutamic acid (PGA), as models of different carbon-backbone structures (polysaccharides, polyesters, and polyamides) produced by bacteria that are suitable for biomedical applications in nanoscale systems. This selection models evidence of the wide versatility of microorganisms to generate biopolymers by diverse metabolic strategies. We highlight the suitability for applied sustainable bioprocesses for the production of BC, PHA, and PGA based on renewable carbon sources and the singularity of each process driven by bacterial machinery. The inherent properties of each polymer can be fine-tuned by means of chemical and biotechnological approaches, such as metabolic engineering and peptide functionalization, to further expand their structural diversity and their applicability as nanomaterials in biomedicine.

scholarly journals Sound propagation in a lined nozzle with shear and bias flows

2018 ◽  
Vol 18 (1) ◽  
pp. 3-48
Author(s):  
LMBC Campos ◽  
C Legendre
Keyword(s):  
Boundary Layer ◽  
Mach Number ◽  
Boundary Layers ◽  
Lower Boundary ◽  
Cross Flow ◽  
Core Flow ◽  
The Core ◽  
Wide Range ◽  
Bias Flow ◽  
Number Formula

In this study, the propagation of waves in a two-dimensional parallel-sided nozzle is considered allowing for the combination of: (a) distinct impedances of the upper and lower walls; (b) upper and lower boundary layers with different thicknesses with linear shear velocity profiles matched to a uniform core flow; and (c) a uniform cross-flow as a bias flow out of one and into the other porous acoustic liner. The model involves an “acoustic triple deck” consisting of third-order non-sinusoidal non-plane acoustic-shear waves in the upper and lower boundary layers coupled to convected plane sinusoidal acoustic waves in the uniform core flow. The acoustic modes are determined from a dispersion relation corresponding to the vanishing of an 8 × 8 matrix determinant, and the waveforms are combinations of two acoustic and two sets of three acoustic-shear waves. The eigenvalues are calculated and the waveforms are plotted for a wide range of values of the four parameters of the problem, namely: (i/ii) the core and bias flow Mach numbers; (iii) the impedances at the two walls; and (iv) the thicknesses of the two boundary layers relative to each other and the core flow. It is shown that all three main physical phenomena considered in this model can have a significant effect on the wave field: (c) a bias or cross-flow even with small Mach number [Formula: see text] relative to the mean flow Mach number [Formula: see text] can modify the waveforms; (b) the possibly dissimilar impedances of the lined walls can absorb (or amplify) waves more or less depending on the reactance and inductance; (a) the exchange of the wave energy with the shear flow is also important, since for the same stream velocity, a thin boundary layer has higher vorticity, and lower vorticity corresponds to a thicker boundary layer. The combination of all these three effects (a–c) leads to a large set of different waveforms in the duct that are plotted for a wide range of the parameters (i–iv) of the problem.

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