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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 32902

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Special Issue Editors

Dr. Sachiyo Aburatani

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Guest Editor

Computational Bio-Big Data Open Innovation Laboratory, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
Interests: network modeling; bioproduction system; gene expression analysis; statistical analysis

Dr. Hiroaki Takaku

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Guest Editor

Department of Applied Life Science, Niigata University of Pharmacy and Applied Life Science, Niigata, Japan
Interests: oleaginous yeast; lipid biosynthesis; lipid droplet; microbial oil; oleochemicals

Dr. Tomokazu Shirai

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Guest Editor

RIKEN center for Sustainable Resource Science, RIKEN, Wako, Japan
Interests: metabolic engineering; synthetic biology; bioinformatics; microbial production

Special Issue Information

Dear Colleagues,

In recent years, the microbial production of materials has been attracting attention for its environmental impact reduction and sustainability. Expanding the abilities of microorganisms is one of the most fascinating and important themes in the bioproduction and bioengineering fields. To improve microorganism capabilities, several types of breeding approaches, such as microbial engineering methods, genetic engineering methods, metabolic engineering methods, synthetic biological methods, and so on, have been developed over the years and applied to construct efficient host strains. However, the information of useful host strain is often tangled with concessions and techniques shared in a limited area. This situation makes bioproduction via microorganisms time-consuming and costly. To accelerate the bioproduction fields via microorganisms, it is necessary to integrate and utilize the several technologies developed by various microorganisms and take advantage of the knowledge acquired.

The aim of this Special Issue of Microorganisms is to present a collection of articles and reviews on research in the microorganism bioproduction fields. Manuscripts covering all aspects of research relating to microorganisms for bioproduction, including every microorganism, empirical techniques, theoretical methods, and computational approaches, are welcome. Of course, new insights into microorganism ability are also invited, and works from applied viewpoints through to fundamental questions related to this field are suitable. This Special Issue aims to serve as a multidisciplinary platform for exchanging valuable information that aids the advancement of the microbial production field.

Dr. Sachiyo Aburatani
Dr. Hiroaki Takaku
Dr. Tomokazu Shirai
Guest Editors

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Keywords

microbial production
microbial engineering
genetic engineering
metabolic engineering
applied microbiology
synthetic biology
microbial fermentation

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Published Papers (9 papers)

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Research

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10 pages, 1311 KiB

Open AccessCommunication

Biosynthetic Gene Clusters from Swine Gut Microbiome

by Leli Wang, Yiru Zhang, Juan Xu, Chuni Wang, Lanmei Yin, Qiang Tu, Huansheng Yang and Jia Yin

Microorganisms 2023, 11(2), 434; https://doi.org/10.3390/microorganisms11020434 - 8 Feb 2023

Cited by 3 | Viewed by 1869

Abstract

The abuse of antibiotics has become a serious health challenge in the veterinary field. It creates environmental selection pressure on bacteria and facilitates the rapid spread of antibiotic resistance genes. The speed of discovery and application of cost-effective alternatives to antibiotics is slow in pig production. Natural products from biosynthetic gene clusters (BGCs) represent promising therapeutic agents for animal and human health and have attracted extraordinary passion from researchers due to their ability to participate in biofilm inhibition, stress resistance, and the killing of competitors. In this study, we detected the presence of diverse secondary metabolite genes in porcine intestines through sequence alignment in the antiSMASH database. After comparing variations in microbial BGCs’ composition between the ileum and the colon, it was found that the abundance of the resorcinol gene cluster was elevated in the ileal microbiome, whereas the gene cluster of arylpolyene was enriched in the colonic microbiome. The investigation of BGCs’ diversity and composition differences between the ileal and colonic microbiomes provided novel insights into further utilizing BGCs in livestock. The importance of BGCs in gut microbiota deserves more attention for promoting healthy swine production. Full article

(This article belongs to the Special Issue Microorganisms Possibility for Future Bioproduction)

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16 pages, 1634 KiB

Open AccessArticle

Culturable Screening of Plant Growth-Promoting and Biocontrol Bacteria in the Rhizosphere and Phyllosphere of Wild Rice

by Zongmu Yao, Yalin Chen, Shouyang Luo, Jilin Wang, Jiafan Zhang, Jianfeng Zhang, Chunjie Tian and Lei Tian

Microorganisms 2022, 10(7), 1468; https://doi.org/10.3390/microorganisms10071468 - 20 Jul 2022

Cited by 7 | Viewed by 2714

Abstract

Wild rice is an important improved resource for cultivated rice and its unique ability to resist biotic and abiotic stress has attracted the attention of many scholars. The microbial community structure in the rhizosphere and leaf area of different rice varieties is also different, which may be one of the reasons for the difference in stress resistance between wild rice and cultivated rice. Forty-six bacteria were screened from the rhizosphere and phyllospheric of four different wild rice varieties. The results of functions of the screened strains showed that 18 strains had a good inhibitory effect on rice blast, and 33 strains had the ability to dissolve phosphorus, potassium, or fix nitrogen. Through potted experiment, the three bacterial strains, 499G2 (Peribacillus simplex), 499G3 (Bacillus velezensis), and 499G4 (B. megaterium) have a positive effect on the growth of cultivated rice in addition to the resistance to rice blast. The contents of total nitrogen, total phosphorus, total potassium, indole acetic acid (IAA), and chlorophyll in plant leaves were increased. In addition, in the verification test of rice blast infection, the application of inoculants can significantly reduce the content of malondialdehyde (MDA), increase the content of soluble sugar, and increase the activity of plant antioxidant enzymes, which may thereby improve rice in resisting to rice blast. Full article

(This article belongs to the Special Issue Microorganisms Possibility for Future Bioproduction)

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13 pages, 4455 KiB

Open AccessArticle

Hrip1 Induces Systemic Resistance against Bean Aphid (Megoura japonica Matsumura) in Common Beans (Phaseolus vulgaris L.)

by Khadija Javed, Yong Wang, Humayun Javed, Talha Humayun and Ayesha Humayun

Microorganisms 2022, 10(6), 1080; https://doi.org/10.3390/microorganisms10061080 - 24 May 2022

Cited by 6 | Viewed by 1842

Abstract

The emerging elicitor protein Hrip1 was evaluated for sublethal effects and biocontrol potential in the common bean Phaseolus vulgaris. In Megoura japonica Matsumura, purified elicitor protein Hrip1 was investigated for impacts on endurance, life expectancy, juvenile expansion, fully grown procreative performance, and pathogen–pest interface. The multi-acting entomopathogenic effects of the active compounds of Alternaria tenuissima active on Hrip1 in common bean (Phaseolus vulgaris L.) plants were also investigated. Megoura japonica population expansion was reduced by Hrip1 treatments (second and third generations). In a host selection test, control plants colonized quicker than Hrip1-treated P. vulgaris plants. Hrip1 influenced the longevity, development, and fertility of insects. Hrip1-elicitor protein concentrations aided M. japonica nymph development. Similarly, seedlings treated with Hrip1 generated fewer offspring than seedlings not treated with Hrip1. Hrip1 altered plant height and leaf surface structure, reducing M. japonica reproduction and colonization. Hrip1-treated P. vulgaris seedlings exhibited somewhat increased amounts of jasmonic acid, salicylic acid, and ethylene (ET). The integrated management of insect pests and biocontrol with Hrip1 in the agroecosystem appears to be suitable against M. japonica based on these findings. Full article

(This article belongs to the Special Issue Microorganisms Possibility for Future Bioproduction)

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18 pages, 1573 KiB

Open AccessArticle

Citrate-Mediated Acyl-CoA Synthesis Is Required for the Promotion of Growth and Triacylglycerol Production in Oleaginous Yeast Lipomyces starkeyi

by Rikako Sato, Satoshi Ara, Harutake Yamazaki, Koji Ishiya, Sachiyo Aburatani and Hiroaki Takaku

Microorganisms 2021, 9(8), 1693; https://doi.org/10.3390/microorganisms9081693 - 9 Aug 2021

Cited by 10 | Viewed by 3273

Abstract

The oleaginous yeast Lipomyces starkeyi is an excellent producer of triacylglycerol (TAG) as a feedstock for biodiesel production. To understand the regulation of TAG synthesis, we attempted to isolate mutants with decreased lipid productivity and analyze the expression of TAG synthesis-related genes in this study. A mutant with greatly decreased lipid productivity, sr22, was obtained by an effective screening method using Percoll density gradient centrifugation. The expression of citrate-mediated acyl-CoA synthesis-related genes (ACL1, ACL2, ACC1, FAS1, and FAS2) was decreased in the sr22 mutant compared with that of the wild-type strain. Together with a notion that L. starkeyi mutants with increased lipid productivities had increased gene expression, there was a correlation between the expression of these genes and TAG synthesis. To clarify the importance of citrate-mediated acyl-CoA synthesis pathway on TAG synthesis, we also constructed a strain with no ATP-citrate lyase responsible for the first reaction of citrate-mediated acyl-CoA synthesis and investigated the importance of ATP-citrate lyase on TAG synthesis. The ATP-citrate lyase was required for the promotion of cell growth and TAG synthesis in a glucose medium. This study may provide opportunities for the development of an efficient TAG synthesis for biodiesel production. Full article

(This article belongs to the Special Issue Microorganisms Possibility for Future Bioproduction)

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20 pages, 6551 KiB

Open AccessArticle

Comprehensive Profiling of Microbiologically Induced CaCO₃ Precipitation by Ureolytic Bacillus Isolates from Alkaline Soils

by Olja Šovljanski, Lato Pezo, Jovana Stanojev, Branimir Bajac, Sabina Kovač, Elvira Tóth, Ivan Ristić, Ana Tomić, Aleksandra Ranitović, Dragoljub Cvetković and Siniša Markov

Microorganisms 2021, 9(8), 1691; https://doi.org/10.3390/microorganisms9081691 - 9 Aug 2021

Cited by 21 | Viewed by 3606

Abstract

Microbiologically induced CaCO₃ precipitation (MICP) is a well-known bio-based solution with application in environmental, geotechnical, and civil engineering. The significance of the MICP has increased explorations of process efficiency and specificity via natural bacterial isolates. In this study, comprehensive profiling of five soil ureolytic Bacillus strains was performed through a newly formed procedure that involved six steps from selection and identification, through kinetic study, to the characterization of the obtained precipitates, for the first time. To shorten the whole selection procedure of 43 bioagents with the MICP potential, Standard Score Analysis was performed and five selected bacteria were identified as Bacillus muralis, B. lentus, B. simplex, B. firmus, and B. licheniformis by the MALDI-TOF mass spectrometry. Despite following the targeted activity, kinetic studies were included important aspects of ureolysis and the MICP such as cell concentration, pH profiling, and reduction in calcium ion concentration. At the final step, characterization of the obtained precipitates was performed using FTIR, XRD, Raman, DTA/TGA, and SEM analysis. Although all tested strains showed significant potential in terms of precipitation of calcite or calcite and vaterite phase, the main differences in the MICP behavior can be observed at the bacterial strain level. B. licheniformis showed favorable behavior compared to the reference Sporosarcina pasteurii DSM 33. Full article

(This article belongs to the Special Issue Microorganisms Possibility for Future Bioproduction)

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12 pages, 1910 KiB

Open AccessArticle

Microbial Production of Bioactive Retinoic Acid Using Metabolically Engineered Escherichia coli

by Minjae Han and Pyung Cheon Lee

Microorganisms 2021, 9(7), 1520; https://doi.org/10.3390/microorganisms9071520 - 16 Jul 2021

Cited by 11 | Viewed by 3790

Abstract

Microbial production of bioactive retinoids, including retinol and retinyl esters, has been successfully reported. Previously, there are no reports on the microbial biosynthesis of retinoic acid. Two genes (blh_SR and raldh_HS) encoding retinoic acid biosynthesis enzymes [β-carotene 15,15′-oxygenase (Blh) and retinaldehyde dehydrogenase2 (RALDH2)] were synthetically redesigned for modular expression. Co-expression of the blh_SR and raldh_HS genes on the plasmid system in an engineered β-carotene-producing Escherichia coli strain produced 0.59 ± 0.06 mg/L of retinoic acid after flask cultivation. Deletion of the ybbO gene encoding a promiscuous aldehyde reductase induced a 2.4-fold increase in retinoic acid production to 1.43 ± 0.06 mg/L. Engineering of the 5’-UTR sequence of the blh_SR and raldh_HS genes enhanced retinoic acid production to 3.46 ± 0.16 mg/L. A batch culture operated at 37 °C, pH 7.0, and 50% DO produced up to 8.20 ± 0.05 mg/L retinoic acid in a bioreactor. As the construction and culture of retinoic acid–producing bacterial strains are still at an early stage in the development, further optimization of the expression level of the retinoic acid pathway genes, protein engineering of Blh and RALDH2, and culture optimization should synergistically increase the current titer of retinoic acid in E. coli. Full article

(This article belongs to the Special Issue Microorganisms Possibility for Future Bioproduction)

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22 pages, 3439 KiB

Open AccessArticle

CRISPRi-Library-Guided Target Identification for Engineering Carotenoid Production by Corynebacterium glutamicum

by Vanessa L. Göttl, Ina Schmitt, Kristina Braun, Petra Peters-Wendisch, Volker F. Wendisch and Nadja A. Henke

Microorganisms 2021, 9(4), 670; https://doi.org/10.3390/microorganisms9040670 - 24 Mar 2021

Cited by 18 | Viewed by 4559

Abstract

Corynebacterium glutamicum is a prominent production host for various value-added compounds in white biotechnology. Gene repression by dCas9/clustered regularly interspaced short palindromic repeats (CRISPR) interference (CRISPRi) allows for the identification of target genes for metabolic engineering. In this study, a CRISPRi-based library for the repression of 74 genes of C. glutamicum was constructed. The chosen genes included genes encoding enzymes of glycolysis, the pentose phosphate pathway, and the tricarboxylic acid cycle, regulatory genes, as well as genes of the methylerythritol phosphate and carotenoid biosynthesis pathways. As expected, CRISPRi-mediated repression of the carotenogenesis repressor gene crtR resulted in increased pigmentation and cellular content of the native carotenoid pigment decaprenoxanthin. CRISPRi screening identified 14 genes that affected decaprenoxanthin biosynthesis when repressed. Carotenoid biosynthesis was significantly decreased upon CRISPRi-mediated repression of 11 of these genes, while repression of 3 genes was beneficial for decaprenoxanthin production. Largely, but not in all cases, deletion of selected genes identified in the CRISPRi screen confirmed the pigmentation phenotypes obtained by CRISPRi. Notably, deletion of pgi as well as of gapA improved decaprenoxanthin levels 43-fold and 9-fold, respectively. The scope of the designed library to identify metabolic engineering targets, transfer of gene repression to stable gene deletion, and limitations of the approach were discussed. Full article

(This article belongs to the Special Issue Microorganisms Possibility for Future Bioproduction)

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Review

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25 pages, 844 KiB

Open AccessReview

Nutrient-Limited Operational Strategies for the Microbial Production of Biochemicals

by Hemshikha Rajpurohit and Mark A. Eiteman

Microorganisms 2022, 10(11), 2226; https://doi.org/10.3390/microorganisms10112226 - 10 Nov 2022

Cited by 17 | Viewed by 3538

Abstract

Limiting an essential nutrient has a profound impact on microbial growth. The notion of growth under limited conditions was first described using simple Monod kinetics proposed in the 1940s. Different operational modes (chemostat, fed-batch processes) were soon developed to address questions related to microbial physiology and cell maintenance and to enhance product formation. With more recent developments of metabolic engineering and systems biology, as well as high-throughput approaches, the focus of current engineers and applied microbiologists has shifted from these fundamental biochemical processes. This review draws attention again to nutrient-limited processes. Indeed, the sophisticated gene editing tools not available to pioneers offer the prospect of metabolic engineering strategies which leverage nutrient limited processes. Thus, nutrient- limited processes continue to be very relevant to generate microbially derived biochemicals. Full article

(This article belongs to the Special Issue Microorganisms Possibility for Future Bioproduction)

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20 pages, 1446 KiB

Open AccessReview

Fermentation of Microalgal Biomass for Innovative Food Production

by Cristiana Garofalo, Alessandra Norici, Lorenzo Mollo, Andrea Osimani and Lucia Aquilanti

Microorganisms 2022, 10(10), 2069; https://doi.org/10.3390/microorganisms10102069 - 19 Oct 2022

Cited by 25 | Viewed by 5394

Abstract

Fermentation is an ancient method used worldwide to process and preserve food while enhancing its nutraceutical profile. Alga-based fermented products have recently been developed and tested due to growing interest in healthy sustainable diets, which demands the development of innovative practices in food production, operating for both human health and Earth sustainability. Algae, particularly microalgae such as Arthrospira platensis, Chlorella vulgaris, and Dunaliella salina, are already cultivated as sources of food due to their valuable compounds, including proteins, pigments, lipids, carotenoids, polyunsaturated fatty acids, steroids, and vitamins. Due to their nutritional composition, functional diversity, and flexible metabolism, microalgae represent good fermentation substrates for lactic acid bacteria (LAB) and yeasts. This review presents an overview of the scientific studies on microalga fermentation underlining microalgae’s properties and health benefits coupled with the advantages of LAB and yeast fermentation. The potential applications of and future perspectives on such functional foods are discussed. Full article

(This article belongs to the Special Issue Microorganisms Possibility for Future Bioproduction)

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