Comparative Genomics of
            <i>Exiguobacterium</i>
            Reveals What Makes a Cosmopolitan Bacterium

Zhang, De-Chao; Zhu, Zhaolu; Li, Yangjie; Li, Xudong; Guan, Ziyu; Zheng, Jinshui

doi:10.1128/msystems.00383-21

Cited by 26 publications

(16 citation statements)

References 94 publications

(104 reference statements)

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“…has been confirmed to have a degradation and metabolizing effect. These results show strong evidence that members of the genus Exiguobacterium could utilize and metabolize various proteins and polysaccharides from environments (D. Zhang et al, 2021).…”

Section: Introductionmentioning

confidence: 70%

“…These group bacteria are isolated from soils, sediments, seawater, permafrost, glaciers, industrial waste, and hydrothermal vents. This bacterial family comprises 25 genera and can survive in various environmental conditions (D. Zhang et al, 2021). One of the unique features of this bacterium is its ability to produce an extremely stable protease enzyme that can work in a wide range of temperatures and pH levels.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Study on The Low-Temperature Active Alkaline Serine Protease Production Capacity and Detergent Application Potential of Novel Exiguobacterium indicum 1.2.3

KATI

2023

Preprint

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Microorganisms have long captivated researchers for their potential to produce enzymes with diverse industrial applications. Efficient production of proteases from new strains is crucial as these enzymes play a vital role in breaking down protein bonds, enabling their use in industrial applications. Therefore, a novel Exiguobacterium indicum 1.2.3 was isolated (Istanbul, Turkiye) and characterized in this study. This strain produced alkaline serine protease, which works in lower temperatures (20-40°C) with casein as a specific substrate. The protease was completely stable for 3 hours at 30 °C. The enzyme was also highly stable in the pH range 811. The optimum activity was obtained at pH 10. The crude enzyme activity was enhanced by various metal ions and retained 147%, 125%, 124%, and 117% of its activity within 1 mM Ca2+, Mn2+, Cu2+, and Mg2+, respectively. The crude enzyme was inactive with PMSF, indicating a serine residue on the active side. The enzyme exhibited a great proteolytic effect in the presence of surfactants and oxidizing agents. The addition of Tween 80, Triton X-100, and sodium perborate improved enzymatic activity up to 135%, 109%, and 105%, respectively. According to the washing results, the crude enzyme effectively removed the blood on different types of standard pre-stained textiles at 30 °C. In conclusion, Exiguobacterium indicum 1.2.3 is a promising candidate for protease production, with its diverse applications spanning various industrial sectors, particularly detergents.

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Section: Introductionmentioning

confidence: 70%

Section: Introductionmentioning

confidence: 99%

Study on The Low-Temperature Active Alkaline Serine Protease Production Capacity and Detergent Application Potential of Novel Exiguobacterium indicum 1.2.3

KATI

2023

Preprint

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“…However, evidence suggests that ARGs may have had roles in cell signal trafficking or were selected for metabolic purposes, as in the case of efflux pumps that have roles in detoxification and act as 'shields' against harmful compounds, not solely antibiotics (Allen et al, 2010). Besides their versatility, ARGs can be highly mobilized throughout microbial populations via transformation, transduction and conjugation, greatly enhancing their dissemination (Zheng et al, 2023). A recent global analysis of topsoil communities showed a widespread prevalence of ARGs worldwide, with efflux pumps being the most common class (Delgado-Baquerizo et al, 2022).…”

Section: Why Do Microorganisms Produce Antibiotics and De Velop Antib...mentioning

confidence: 99%

The antibiotic crisis: On the search for novel antibiotics and resistance mechanisms

Van Goethem,

Marasco,

Hong

et al. 2024

Microbial Biotechnology

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In the relentless battle for human health, the proliferation of antibiotic‐resistant bacteria has emerged as an impending catastrophe of unprecedented magnitude, potentially driving humanity towards the brink of an unparalleled healthcare crisis. The unyielding advance of antibiotic resistance looms as the foremost threat of the 21st century in clinical, agricultural and environmental arenas. Antibiotic resistance is projected to be the genesis of the next global pandemic, with grim estimations of tens of millions of lives lost annually by 2050. Amidst this impending calamity, our capacity to unearth novel antibiotics has languished, with the past four decades marred by a disheartening ‘antibiotic discovery void’. With nearly 80% of our current antibiotics originating from natural or semi‐synthetic sources, our responsibility is to cast our investigative nets into uncharted ecological niches teeming with microbial strife, the so‐called ‘microbial oases of interactions’. Within these oases of interactions, where microorganisms intensively compete for space and nutrients, a dynamic and ever‐evolving microbial ‘arms race’ is constantly in place. Such a continuous cycle of adaptation and counter‐adaptation is a fundamental aspect of microbial ecology and evolution, as well as the secrets to unique, undiscovered antibiotics, our last bastion against the relentless tide of resistance. In this context, it is imperative to invest in research to explore the competitive realms, like the plant rhizosphere, biological soil crusts, deep sea hydrothermal vents, marine snow and the most modern plastisphere, in which competitive interactions are at the base of the microorganisms' struggle for survival and dominance in their ecosystems: identify novel antibiotic by targeting microbial oases of interactions could represent a ‘missing piece of the puzzle’ in our fight against antibiotic resistance.

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“…Genomic DNA was extracted, a paired-end library was constructed for each genome, and sequencing was performed as previously described [23]. The raw reads of each genome were processed for removal of low-quality bases and adaptors, using Trimmomatic v0.36 [24].…”

Section: Genome Sequencing Assembly and Annotation Of Nitratereducing...mentioning

confidence: 99%

The diversity and metabolism of culturable nitrate-reducing bacteria from the photic zone of the Western North Pacific Ocean

Jiang¹,

Liu

Zhang³

et al. 2023

Preprint

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To better understand bacterial communities and metabolism under nitrogen deficiency, 154 seawater samples were obtained from 0-200 m at 22 stations in the photic zone of the Western North Pacific Ocean and, from them, 634 nitrate-utilizing bacteria were isolated using selective media and culture-dependent methods. Twenty-nine of 94 representative nitrate-utilizing isolates were found to be nitrate reducers, among which Qipengyuania flava, Roseibium aggregatum, Erythrobacter aureus, Vibrio campbellii, and Stappia indica were identified from all tested seawater layers of the photic zone and at almost all stations. The presence of multiple genes for chitin degradation and extracellular peptidases may indicate that almost all nitrate-reducing isolates (28/29) can use chitin and proteinaceous compounds as important sources of carbon and nitrogen. Most strains contained assimilatory nitrate reduction or dissimilatory nitrate reduction to ammonia genes suggesting that nitrate and nitrite could act as electron acceptors to generate ammonia. All of the nitrate-reducing isolates contained genes encoding the assimilatory sulfate reduction pathway, and six of the nitrate-reducing isolates encoded sulfur oxidization genes, indicating that they could oxidize sulfur. Five nitrate-reducing isolates obtained near the chlorophyll a-maximum layer contained a dimethylsulfoniopropionate synthesis gene and three of them contained both dimethylsulfoniopropionate synthesis and cleavage genes. This suggests that nitrate-reducing isolates may participate in dimethylsulfoniopropionate synthesis and catabolism in photic seawater. Collectively, these results reveal nitrate-reducing bacterial diversity and have implications for understanding the role of such strains in the ecology and biogeochemical cycles of nitrogen, carbon, and sulfur in the oligotrophic marine photic zone.

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Comparative Genomics of Exiguobacterium Reveals What Makes a Cosmopolitan Bacterium

Cited by 26 publications

References 94 publications

Study on The Low-Temperature Active Alkaline Serine Protease Production Capacity and Detergent Application Potential of Novel Exiguobacterium indicum 1.2.3

Study on The Low-Temperature Active Alkaline Serine Protease Production Capacity and Detergent Application Potential of Novel Exiguobacterium indicum 1.2.3

The antibiotic crisis: On the search for novel antibiotics and resistance mechanisms

The diversity and metabolism of culturable nitrate-reducing bacteria from the photic zone of the Western North Pacific Ocean

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