Complete genome sequence of Enterobacter sp. IIT-BT 08: A potential microbial strain for high rate hydrogen production

Genome mining discovery of hydrogen production pathway of Klebsiella sp. WL1316 fermenting cotton stalk hydrolysate

Genome sequencing was used to identify key genes for the generation of hydrogen gas through cotton stalk hydrolysate fermentation by Klebsiella sp. WL1316. Genome annotation indicated that the genome size was 5.2 Mb with GC content 57.6%. Xylose was metabolized in the pentose phosphate pathway via the conversion of xylose to xylulose in Klebsiella sp. WL1316. This strain contained diverse formate-hydrogen lyases and hydrogenases with gene numbers higher than closely related species. A metabolic network involving glucose, xylose utilisation, and fermentative hydrogen production was reconstructed. Metabolic analysis of key node metabolites showed that glucose and xylose metabolism influenced biomass synthesis and biohydrogen production. Formic acid accumulated during fermentation at 24-48 h but decreased sharply after 48 h, illustrating the splitting of formic acid to hydrogen gas during early-to-mid fermentation. The Kreb's cycle was the main competitive metabolic branch of biohydrogen synthesis at 24 h of fermentation. Lactic and acetic acid fermentation and late ethanol accumulation competed the carbon skeleton of biohydrogen synthesis after 72 h of fermentation, indicating that these competitive pathways are regulated in middle-to-late fermentation (48-96 h). This study is the first to elucidate the metabolic mechanisms of mixed sugar utilisation and biohydrogen synthesis based on genomic information.

Wide Distribution and Specific Resistance Pattern to Third-Generation Cephalosporins of Enterobacter cloacae Complex Members in Humans and in the Environment in Guadeloupe (French West Indies)

Species belonging to Enterobacter cloacae complex have been isolated in numerous environments and samples of various origins. They are also involved in opportunistic infections in plants, animals, and humans. Previous prospection in Guadeloupe (French West Indies) indicated a high frequency of E. cloacae complex strains resistant to third-generation cephalosporins (3GCs) in a local lizard population (Anolis marmoratus), but knowledge of the distribution and resistance of these strains in humans and the environment is limited. The aim of this study was to compare the distribution and antibiotic susceptibility pattern of E. cloacae complex members from different sources in a “one health” approach and to find possible explanations for the high level of resistance in non-human samples. E. cloacae complex strains were collected between January 2017 and the end of 2018 from anoles, farm animals, local fresh produce, water, and clinical human samples. Isolates were characterized by the heat-shock protein 60 gene-fragment typing method, and whole-genome sequencing was conducted on the most frequent clusters (i.e., C-VI and C-VIII). The prevalence of resistance to 3GCs was relatively high (56/346, 16.2%) in non-human samples. The associated resistance mechanism was related to an AmpC overproduction; however, in human samples, most of the resistant strains (40/62) produced an extended-spectrum beta-lactamase. No relation was found between resistance in isolates from wild anoles (35/168) and human activities. Specific core-genome phylogenetic analysis highlighted an important diversity in this bacterial population and no wide circulation among the different compartments. In our setting, the mutations responsible for resistance to 3GCs, especially in ampD, were diverse and not compartment specific. In conclusion, high levels of resistance in non-human E. cloacae complex isolates are probably due to environmental factors that favor the selection of these resistant strains, and this will be explored further.

Population structure and pangenome analysis of Enterobacter bugandensis uncover the presence of blaCTX-M-55, blaNDM-5 and blaIMI-1, along with sophisticated iron acquisition strategies

Enterobacter bugandensis is a recently described species that has been largely associated with nosocomial infections. We report the genome of a non-clinical E. bugandensis strain, which was integrated with publicly available genomes to study the pangenome and general population structure of E. bugandensis. Core- and whole-genome multilocus sequence typing allowed the detection of five E. bugandensis phylogroups (PG-A to E), which contain important antimicrobial resistance and virulence determinants. We uncovered several extended-spectrum β-lactamases, including bla_CTX-M-55 and bla_NDM-5, present in an IncX replicon type plasmid, described here for the first time in E. bugandensis. Genetic context analysis of bla_NDM-5 revealed the resemblance of this plasmid with other IncX plasmids from other bacteria from the same country. Three distinctive siderophore producing operons were found in E. bugandensis: enterobactin (ent), aerobactin (iuc/iut), and salmochelin (iro). Our findings provide novel insights on the lifestyle, physiology, antimicrobial, and virulence profiles of E. bugandensis.

Microbial cell immobilization in biohydrogen production: a short overview

The high dependence on fossil fuels has escalated the challenges of greenhouse gas emissions and energy security. Biohydrogen is projected as a future alternative energy as a result of its non-polluting characteristics, high energy content (122 kJ/g), and economic feasibility. However, its industrial production has been hampered by several constraints such as low process yields and the formation of biohydrogen-competing reactions. This necessitates the search for other novel strategies to overcome this problem. Cell immobilization technology has been in existence for many decades and is widely used in various processes such as wastewater treatment, food technology, and pharmaceutical industry. In recent years, this technology has caught the attention of many researchers within the biohydrogen production field owing to its merits such as enhanced process yields, reduced microbial contamination, and improved homogeneity. In addition, the use of immobilization in biohydrogen production prevents washout of microbes, stabilizes the pH of the medium, and extends microbial activity during continuous processes. In this short review, an insight into the potential of cell immobilization is presented. A few immobilization techniques such as entrapment, adsorption, encapsulation, and synthetic polymers are discussed. In addition, the effects of process conditions on the performance of immobilized microbial cells during biohydrogen production are discussed. Finally, the review concludes with suggestions on improvement of cell immobilization technologies in biohydrogen production.

High quality genome sequence and description of Enterobacter mori strain 5-4, isolated from a mixture of formation water and crude-oil

Enterobacter mori strain 5-4 is a Gram-negative, motile, rod shaped, and facultatively anaerobic bacterium, which was isolated from a mixture of formation water (also known as oil-reservior water) and crude-oil in Karamay oilfield, China. To date, there is only one E. mori genome has been sequenced and very little knowledge about the mechanism of E. mori adapted to the petroleum reservoir. Here, we report the second E. mori genome sequence and annotation, together with the description of features for this organism. The 4,621,281 bp assembly genome exhibits a G + C content of 56.24% and contains 4,317 protein-coding and 65 RNA genes, including 5 rRNA genes.