Preface

The recent breakthrough in microbial studies has applied next-generation sequencing (NGS), a massive omics analysis, to the composition and structure of microbial communities. NGS can identify microbes without the need for their cultivation. Their mere presence can be ascertained and often quantitated, and even their metabolic capabilities of microbial constituents predicted. This breakthrough led to an explosive growth in research on microbes.

Many important advances have been made in human health-related studies. Indeed, gut microbial communities have been extensively analyzed and differences between healthy and diseased microbiomes have been determined. Studies of the effects of changes of diet, of antibiotic treatments, and of probiotics on the gut microbiome have been published. It was found that the human gut microbiome varies significantly from individual to individual, and longitudinal studies have shown the major effects of antibiotics as well as the time course of return to a "normal," healthy microbiome.

Ethnic and geographical influences have been analyzed. While most studies focused on individuals in the Western world and their corresponding diet, comparisons with less accessible communities have been very informative. In particular, analyses of indigenous communities, never exposed to antibiotics, have illuminated the effects of their wide use. In other studies it was found, for example, that the use of antibiotics in early childhood can have life-long consequences, perhaps predisposing to allergic and atopic sequelae.

Similar microbiome studies have been performed on human skin, oral cavities, and genitals. Different sites of the human body carry different niche-specific microbiota. Dry, moist, sebaceous, UV-exposed, and protected regions of skin all have different microbiota. The immense interpersonal variation precludes describing a "healthy" skin microbiome; however, one's skin microbiomes tend to be stable over time. Interestingly, the effects of hygiene products, soaps and deodorants, are apparently underwhelming and transient. Human skin and the oral cavity contain very rich and varied microbiomes with myriad species. In contrast, vaginal microbiomes in the posterior fornix tend to have a limited number of species, nearly monoclonal lactobacilli environment.

Specific research has been devoted to human pathogens, their mechanisms of causing disease, and the potentials for their management and alleviation. For example, eczema, atopic dermatitis, is associated with overgrowth of *Staphylococcus aureus*. In contrast, psoriasis, another inflammatory skin disease, is not specifically associated with a particular microbiome.

Interestingly, the richness and interpersonal differences in human microbiomes are equalized by the metabolic capabilities of such microbiomes. In other words, while the compositions of the microbiomes vary greatly, the overall metabolic processes, synthesis, and degradation of nutrients and other natural products do not vary much; different assemblies of microorganism can perform similar tasks.

**II**

**Chapter 8 153**

**Chapter 9 167**

**Chapter 10 193**

**Chapter 11 219**

Industrial Uses **241**

**Chapter 12 243**

**Chapter 13 261**

**Chapter 14 275**

New Approaches for Competing Microbial Resistance and Virulence *by Mohammed El-Mowafy, Abdelaziz Elgaml and Mona Shaaban*

Gut-to-Brain Axis: Relationship with Autism Spectrum Disorders

*by José Maria Rodrigues da Luz, Marliane de Cássia Soares da Silva, Leonardo Ferreira dos Santos and Maria Catarina Megumi Kasuya*

Probiotics and Bioremediation

*by Qomarudin Helmy, Edwan Kardena and Sri Gustiani*

Virulence Determinants of Non-typhoidal *Salmonellae*

Interplay between Human Intestinal Microbiota and

*by Francisco Javier Díaz-García, Saúl Flores-Medina* 

Bioconversion of Weedy Waste into Sugary Wealth *by Prajakta Prakash Kamble, Suresh Shivaji Suryawanshi, Maheshkumar Vishnu Kore, Nahid Irani, Jyoti Prafulla Jadhav* 

Microorganisms as Biocatalysts and Enzyme Sources *by Arturo Cano-Flores, Javier Gómez, Iker S. Escalona-Torres* 

*and Diana Mercedes Soriano-Becerril*

Plastics Polymers Degradation by Fungi

*and Benjamín Velasco-Bejarano*

**Section 4**

*and Yasmin Chand Attar*

*by Ruimin Gao, Linru Wang and Dele Ogunremi*

The increased understanding of microbial communities led to attempts to use microbes as antagonists of pathogens, i.e. as treatments. For example, fecal transplants are used in the treatment of *Clostridium difficile* infections, a serious nosocomial challenge. Identification of gut microbial influence on mood and brain function may yield corresponding neurological therapies. The gut microbiome is known to influence the metabolism of various drugs and chemicals, e.g. cytostatic medications in cancer treatment, making some patients less sensitive to chemotherapy.

The microbiome studies of natural habitats, terrestrial and aquatic, have benefited from NGS methodology. Such studies revealed that large-scale chemical transformations can occur in oceans and seas due to microorganisms. Similarly, nutrient cycles in microbiota in various tropical habitats have been described.

The remarkable growth of microbial DNA sequence databases has provided a background for novel uses of microbes in industrial processes, either for the synthesis of important compounds or for the degradation and handling of waste. Microbial production of specific enzymes for industrial uses is an interesting option.

In this volume, chapters dealing with the cutting-edge research in all these fields are presented.

> **Miroslav Blumenberg** New York University Langone Medical Center, USA
