Microbiome-Host Interactions

D. Dhanasekaran, Dhiraj Paul, N. Amaresan, A. Sankaranarayanan, Yogesh S. Shouche, D. Dhanasekaran, Dhiraj Paul, N. Amaresan, A. Sankaranarayanan, Yogesh S. Shouche

• Publisher: CRC Press
• Year: 2021
• ISBN:
  9781000353143
• Edition: 1
• Topic: Medicina
• Subtopic: Biotecnología en medicina

Microbiota are a promising and fascinating subject in biology because they integrate the microbial communities in humans, animals, plants, and the environment. In humans, microbiota are associated with the gut, skin, and genital, oral, and respiratory organs. The plant microbial community is referred to as "holobiont, " and it is influential in the maintenance and health of plants, which themselves play a role in animal health and the environment.

The contents of Microbiome-Host Interactions cover all areas as well as new research trends in the fields of plant, animal, human, and environmental microbiome interactions. The book covers microbiota in polar soil environments, in health and disease, in Caenorhabditis elegans, and in agroecosystems, as well as in rice root and actinorhizal root nodules, speleothems, and marine shallow-water hydrothermal vents.

Moreover, this book provides comprehensive accounts of advanced next-generation DNA sequencing, metagenomic techniques, high-throughput 16S rRNA sequencing, and understanding nucleic acid sequence data from fungal, algal, viral, bacterial, cyanobacterial, actinobacterial, and archaeal communities using QIIME software (Quantitative Insights into Microbial Ecology).

FEATURES

• 
  
  

• Summarizes recent insight in microbiota and host interactions in distinct habitats, including Antarctic, hydrothermal vents, speleothems, oral, skin, gut, feces, reproductive tract, soil, root, root nodules, forests, and mangroves

• 
  
  

• Illustrates the high-throughput amplicon sequencing, computational techniques involved in the microbiota analysis, downstream analysis and visualization, and multivariate analysis commonly used for microbiome analysis

• 
  
  

• Describes probiotics and prebiotics in the composition of the gut microbiota, skin microbiome impact in dermatologic disease prevention, and microbial communities in the reproductive tract of humans and animals

• 
  
  

• Presents information in a reachable way for students, teachers, researchers, microbiologists, computational biologists, and other professionals who are interested in strengthening or enlarging their knowledge about microbiome analysis with next-generation DNA sequencing in the different branches of the sciences

1

An Insight of Microbiome Science

T. Savitha

Tiruppur Kumaran College for Women

A. Sankaranarayanan

Uka Tarsadia University

Ashraf Y. Z. Khalifa

King Faisal University
University of Beni-Suef

Contents

1.1 Introduction

1.2 Ecological Theory in Understanding of the Microbiome

1.3 Different Types of Microbiome

1.3.1 Microbiome

1.3.2 Types of Microbiome

1.3.2.1 Soil Microbiome

1.3.2.2 Marine Microbiome

1.3.2.3 Animal Microbiome

1.3.2.4 Plant Microbiome

1.3.2.5 Human Microbiome

1.4 Classification of Microbiomes in Human Health

1.4.1 The Skin Microbiome

1.4.2 Oral Microbiome

1.4.3 The Respiratory Microbiome

1.4.4 Gut Microbiome

1.4.5 Genital Microbiome

1.5 Future Perspectives

References

1.1 Introduction

Microbiome is a popular and repeatedly used term due to its widespread activities in various scientific platforms and due to its influential roles. It is sprawling its wings in the diversified fields of biology, and the microbes have a symbiotic and pathogenic association with various biotic organisms, including all vertebrates and plants. It is a great promising tool and that’s the reason in the past decade more than 1.7 billion US $ spent toward human microbiome research (Proctor, 2019). The microbiome science nowadays attracts more researchers due to its importance in diversified fields. Further, the new discoveries and concepts have been emerging from this field changing the perception of the importance of this field among the researchers (Walter and Ley, 2011; O’Callaghan et al., 2016).

Microbiome is defined as a “collective genes and genomes” of all the microorganisms dwelling in a particular environment (Marchesi and Ravel, 2015). Another short definition is, “Microbiome means genes associated with the microbiota” (Amato, et al., 2016). Diversified microbiomes are present in the different parts of body, environment, and other habitats (Gilbert and Stephens, 2018). In addition, their presence depends on the surrounding conditions (Derrien et al., 2019; de Steenhuijsen Piters et al., 2015). There are many factors that are involved in cohabitation of microbiome in biota.

Human microbiome was considered as one among the organs of human body (Baquero and Nombela, 2012), merely a decade ago. The relationship between microbiome and humans starts within 20 minutes after the birth of the infant. The microbiome of the infant resembles the microbiome of mother’s vagina (i.e., infants born through vagina) or that of skin (i.e., infants born through cesarean) (Dominguez-Bello et al., 2010; Rasmussen et al., 2020). Microorganisms are dwelling on the surface and in the tissues of small-sized marine biotic organisms as well as in larger-sized animals. There are possible chances of incorporating microorganisms as a sentinel in the host due to the rapid change in the marine environment by pollution (Ainsworth and Gates, 2016). It is not a surprise to state that around 40 trillion microbial cells reside in, and on the surface of, the human body—especially, more microbial flora are present in the gut (Nagasaka et al., 2020). Microbiomes sprawl their wings and are not restricted only to the gut, skin (Bangert et al., 2011), lower respiratory tract (Charlson et al., 2011), nasal cavity, and oropharynx (Beck et al., 2012; Dickson et al., 2013). As per the report, the highest microbial diversity and density were reported in the gastrointestinal tract followed by the skin.

More than a decade ago, NIH (National Institute of Health) has initiated the human microbiome project and reported the presence of microbiota in different parts of the body. Further, the genome sequence technologies and metagenomic analysis have enhanced the interest of scientists to know the function and various research aspects of microbiome (Amon and Sanderson, 2017). In addition, sequencing techniques, genetic fingerprinting techniques, quantitative polymerase chain reaction (PCR)approach, multilocus gene typing, fluorescent-tagged oligonucleotide probes, and metagenomic gene sequencing approaches are additional techniques to concentrate more on the microbiome-based research studies (O’Callaghan et al., 2016).

Microbiota present in different parts of the plants is called as “plant holobiont/plant microbiome” (Hassani et al., 2018). It plays a pivotal role in supporting the growth and maintenance of plant health (Lindow and Brandl, 2003; Buee et al., 2009; Berendsen et al., 2012; Vorholt, 2012; Hassani et al., 2018) due to its presence in phyllosphere, rhizosphere, endosphere, and episphere (outside) (Dastogeer et al., 2020). The association between plants and microbiome was developed 700 million years ago (Heckman et al., 2001). The various functions rendered by plant microbiome are presented in Figure 1.1. In this juncture, it is a need to mention that the metabolites secreted by bacterial endophytes present in plants showed more efficiency in the growth of the plant than the metabolites secreted by the plants in association with the microbes in open environments (like rhizosphere microbes). The reason is that the metabolites are secreted in open environment, and there are more chances of becoming affected by various extraneous factors such as biotic and abiotic (Santoyo et al., 2017).

FIGURE 1.1 Various functions exerted by microbiome in plants.

For the maintenance of animal health, including humans, the resident microbial communities exert a prominent role. These communities alleviate various chronic diseases, and metabolic and neurobiological diseases; thus, the host microbial traits play a predominant role (Douglas, 2019). A new concept has recently emerged and named as “one health concept,” which insists the relationship between humans and animal environment, and it envisages the shifting of pathogens from animals and environment to human populations (Trinh et al., 2018). Like humans, animal microbiomes influence the health of livestock, disease vectors, and pets. In addition, pet animals share their microbiome diversity with pet owners’ skin (Ross et al., 2017; Song et al., 2013). There exists a strong association between host—especially animals—and microbes; hence, the bonding may be known as “biocenosis” or “living community” (Bosch and Miller, 2016).

The resident microbial communities influence the health and fitness of animals and humans by their presence (Douglas, 2019). In animals, the various functions of gut microbiome were listed elsewhere (O’Callaghan et al., 2016). In animals, the predominant microbial group is bacteria—especially strict anaerobes—followed by also protozoa, viruses, and fungi. The microbiota varies in animals based on the food habit—especially, the rumen of cow and sheep is dominated by fiber-degrading bacteria (Simpson et al., 2002) followed by the methanogenic bacteria (Boomker and Cronje, 2000). In another interesting observation, the specific members of microbiome determined the milk-yielding capacity of animals (Jewell et al., 2015), especially cows.

With the increasing trends of industrialization and urbanization, environmental microbiome plays an important role in the Universe. Due to increasing trends of pollutants, especially air pollutants (Dujardin et al., 2020; Rajagopalan et al., 2018; Huang et al., 2018), fine (Zhang et al., 2017) and particulate matter (Belis et al., 2013), and industrial emissions (Taiwo et al., 2014), the microbiome plays a major role in preventing the deterioration of the health of the human being. In light of the above, this chapter concentrates on the ecological attributes in understanding of the microbiome; classification of microbiomes; various microbiomes in gut, genital tract, skin, oral cavity, and respiratory organs; and future perspectives of microbiome.

1.2 Ecological Theory in Understanding of the Microbiome

Ecological understanding plays a vital role in the microbial assemblages of microbiome. The microbial assemblages formed as community in any biotic/abiotic sources based on dispersal, local diversification, environmental selection, and ecological drift (Costello et al., 2012). For example, the association between the host and gut microbiota depends on host genome, nutrition, and lifestyle of the particular host (Nicholson et al., 2012). The host and the conditions determine what type of microbiota exists in the particular environment. In case of vaginal microbiome, the microbiome compositional changes related to pregnancy and menstruation can lead to diseases like bacterial vaginosis (Greenbaum et al., 2018). In another study about the gut microbiota, the stability of the microbiome members depends on immunosuppression, spatial structuring, and other allied factors related to them (Coyte et al., 2015). The diet and body size affect the microbiome diversity in animals; especially, the physiology of the gut also plays a vital role in microbiome diversity (Reese and Dunn, 2018). Various soil abiotic parameters and competition among microbes play a role in the diversity of microbiome in soil and soil-associated plant rhizospheric environment—especially physical interaction, secretion, and plant immunity (Tkacz et al., 2020).

1.3 Different Types of Microbiome

1.3.1 Microbiome

The first metaphors of human-associated microbiota arose back from the 1670s to the 1680s, when Antonie van Leeuwenhoek started with his newly developed hand-crafted microscopes. In a letter written to the Royal Society of London in 1683, he described and illustrated five different kinds of bacteria (called by him as “animalcules”...