Advances in Applied Microbiology

The early postnatal period represents a critical window of time for the establishment and maturation of the human gut microbiota. The gut microbiota undergoes dramatic developmental changes during the first year of life, being influenced by a variety of external factors, with diet being a major player. Indeed, the introduction of complementary feeding provides novel nutritive substrates and triggers a shift from milk-adapted gut microbiota toward an adult-like bacterial composition, which is characterized by an enhancement in diversity and proportions of fiber-degrading bacterial genera like Ruminococcus, Prevotella, Eubacterium, and Bacteroides genera...

Selenium (Se) is an essential trace element present as selenocysteine (SeCys) in selenoproteins, which have an important role in thyroid metabolism and the redox system in humans. Se deficiency affects between 500 and 1000 million people worldwide. Increasing Se intake can prevent from bacterial and viral infections. Se deficiency has been associated with cancer, Alzheimer, Parkinson, decreased thyroid function, and male infertility. Se intake depends on the food consumed which is directly related to the amount of Se in the soil as well as on its availability...

Kluyveromyces marxianus is a non-Saccharomyces yeast that has gained importance due to its great potential to be used in the food and biotechnology industries. In general, K. marxianus is a known yeast for its ability to assimilate hexoses and pentoses; even this yeast can grow in disaccharides such as sucrose and lactose and polysaccharides such as agave fructans. Otherwise, K. marxianus is an excellent microorganism to produce metabolites of biotechnological interest, such as enzymes, ethanol, aroma compounds, organic acids, and single-cell proteins...

The genome-scale metabolic network model is an effective tool for characterizing the gene-protein-response relationship in the entire metabolic pathway of an organism. By combining various algorithms, the genome-scale metabolic network model can effectively simulate the influence of a specific environment on the physiological state of cells, optimize the culture conditions of strains, and predict the targets of genetic modification to achieve targeted modification of strains. In this review, we summarize the whole process of model building, sort out the various tools that may be involved in the model building process, and explain the role of various algorithms in model analysis...

Cyanobacteria are ubiquitously distributed in nature and are the most abundant photoautotrophs on Earth. Their long evolutionary history reveals that cyanobacteria have a remarkable capacity and strong adaptive tendencies to thrive in a variety of conditions. Thus, they can survive successfully, especially in harsh environmental conditions such as salty environments, high radiation, or extreme temperatures. Among others, salt stress because of excessive salt accumulation in salty environments, is the most common abiotic stress in nature and hampers agricultural growth and productivity worldwide...

Pathogenic fungi are widespread and cause a variety of diseases in human beings and other organisms. At present, limited classes of antifungal agents are available to treat invasive fungal diseases. With the wide use of the commercial antifungal agents, drug resistance of pathogenic fungi are continuously increasing. Therefore, exploring effective antifungal agents with novel drug targets is urgently needed to cope with the challenges that the antifungal area faces. pH homeostasis is vital for multiple cellular processes, revealing the potential for defining novel drug targets...

Methane is abundant in nature, and excessive emissions will cause the greenhouse effect. Methane is also an ideal carbon and energy feedstock for biosynthesis. In the review, the microorganisms, metabolism, and enzymes for methane utilization, and the advances of conversion to value-added bioproducts were summarized. First, the physiological characteristics, classification, and methane oxidation process of methanotrophs were introduced. The metabolic pathways for methane utilization and key intermediate metabolites of native and synthetic methanotrophs were summarized...

The transcription of genes in the yeast Saccharomyces cerevisiae is governed by multiple layers of regulatory elements and proteins, cooperating to ensure optimum expression of the final protein product based on the cellular requirements. Promoters have always been regarded as the most important determinant of gene transcription, but introns also play a key role in the expression of intron-encoding genes. Some introns can enhance transcription when introduced either promoter-proximal or embedded in the open reading frame of genes...

One of the biggest health related issues in the twenty-first century is cancer. The current therapeutic platforms have not advanced enough to keep up with the number of rising cases. The traditional therapeutic approaches frequently fail to produce the desired outcomes. Therefore, developing new and more potent remedies is crucial. Recently, investigating microorganisms as potential anti-cancer treatments have garnered a lot of attention. Tumor-targeting microorganisms are more versatile at inhibiting cancer than the majority of standard therapies...

Bacterial antimicrobial resistance (AMR) is a persisting and growing threat to human health. Characterization of antibiotic resistance genes (ARGs) in the environment is important to understand and control ARG-associated microbial risks. Numerous challenges exist in monitoring ARGs in the environment, due to the extraordinary diversity of ARGs, low abundance of ARGs with respect to the complex environmental microbiomes, difficulties in linking ARGs with bacterial hosts by molecular methods, difficulties in achieving quantification and high throughput simultaneously, difficulties in assessing mobility potential of ARGs, and difficulties in determining the specific AMR determinant genes...

Rhodotorula sp. are well-known for their ability to biosynthesize a diverse range of valuable biomolecules, including carotenoids, lipids, enzymes, and polysaccharides. Despite the high number of studies conducted using Rhodotorula sp. at the laboratory scale, most of these do not address all processual aspects necessary for scaling up these processes for industrial applications. This chapter explores the potential of Rhodotorula sp. as a cell factory for the production of distinct biomolecules, with a particular emphasis on exploring their use from a biorefinery perspective...

Transcriptomics, or more specifically mRNA sequencing, is a powerful tool to study gene expression at the single-cell level (scRNA-seq) which enables new insights into a plethora of biological processes. While methods for single-cell RNA-seq in eukaryotes are well established, application to prokaryotes is still challenging. Reasons for that are rigid and diverse cell wall structures hampering lysis, the lack of polyadenylated transcripts impeding mRNA enrichment, and minute amounts of RNA requiring amplification steps before sequencing...

BioMateriOME evolved from a prototyping process which was informed from discussions between a team of designers, architects and microbiologists, when considering constructing with biomaterials or human cohabitation with novel living materials in the built environment. The prototype has two elements (i) BioMateriOME-Public (BMP), an interactive public materials library, and (ii) BioMateriOME-eXperimental (BMX), a replicated materials library for rigorous microbiome experimentation. The prototype was installed into the OME, a unique experimental living house, in order to (1) gain insights into society's perceptions of living materials, and (2) perform a comparative analysis of indoor surface microbiome development on novel biomaterials in contrast to conventional indoor surfaces, respectively...

A biofilm is a sessile community characterized by cells attached to the surface and organized into a complex structural arrangement. Dental caries is a biofilm-dependent oral disease caused by infection with cariogenic pathogens, such as Streptococcus mutans, and associated with frequent exposure to a sugar-rich diet and poor oral hygiene. The virulence of cariogenic biofilms is often associated with the spatial organization of S. mutans enmeshed with exopolysaccharides on tooth surfaces. However, in the oral cavity, S...

As a semi-essential amino acid, l-arginine (l-Arg) plays an important role in food, health care, and medical treatment. At present, the main method of producing l-Arg is the use of microbial fermentation. Therefore, the selection and breeding of high-efficiency microbial strains is the top priority. To continuously improve the l-Arg production performance of the strains, a series of metabolic engineering strategies have been tried to transform the strains. The production of l-Arg by metabolically engineered Corynebacterium glutamicum (C...

For decades, bacteria were thought of as "bags" of enzymes, lacking organelles and significant subcellular structures. This stood in sharp contrast with eukaryotes, where intracellular compartmentalization and the role of large-scale order had been known for a long time. However, the emerging field of Bacterial Cell Biology has established that bacteria are in fact highly organized, with most macromolecular components having specific subcellular locations that can change depending on the cell's physiological state (Barry & Gitai, 2011; Lenz & Søgaard-Andersen, 2011; Thanbichler & Shapiro, 2008)...

An electromagnetic field (EMF) has been shown to have various stimulatory or inhibitory effects on microorganisms. Over the years, growing interest in this topic led to numerous discoveries suggesting the potential applicability of EMF in biotechnological processes. Among these observations are stimulative effects of this physical influence resulting in intensified biomass production, modification of metabolic activity, or pigments secretion. In this review, we present the current state of the art and underline the main findings of the application of EMF in bioprocessing and their practical meaning in process engineering using examples selected from studies on bacteria, archaea, microscopic fungi and yeasts, viruses, and microalgae...

Temperature-dependent composting is a challenging task but is worthy if it is done in the right manner. Cold composting has been known to be practiced since ancient times but there were not enough advancements to overcome the long mesophilic phase and bring the compost maturation to a short period. The composting processes that have been well practiced are discussed and the role of psychrotrophic bacteria that produce cold tolerant hydrolytic enzymes has been highlighted. In this chapter, the mechanism of substrate degradation has been elaborated to better understand the need of specific bacteria for a specific kind of substrate allowing fast and efficient decomposition...

The term Gain-of-Function (GoF) describes the gain of new functions by organisms through genetic changes, which can naturally occur or by experimental genetic modifications. Gain-of-Function research on viruses is enhancing transmissibility, virus replication, virulence, host range, immune evasion or drug and vaccine resistance to get insights into the viral mechanisms, to create and analyze animal models, to accelerate drug and vaccine development and to improve pandemic preparedness. A subset is the GoF research of concern (GOFROC) on enhanced potentially pandemic pathogens (ePPPs) that could be harmful for humans...

Lactic acid bacteria (LAB) are ubiquitous bacteria associated with spontaneous lactic fermentation of vegetables, dairy and meat products. They are generally recognized as safe (GRAS), and they are involved in transformation of probiotic lacto-fermented foods, highly desired for their nutraceutical properties. The antifungal activity is one of the exciting properties of LAB, because of its possible application in food bio-preservation, as alternative to chemical preservatives. Many recent research works have been developed on antifungal activity of LAB, and they demonstrate their capacity to produce various antifungal compounds, (i...