The human microbiome harbors a diverse array of microbes which establishes a mutually beneficial relation with the host in healthy conditions, however, the dynamic homeostasis is influenced by both host and environmental factors. Smoking contributes to modifications of the oral, lung and gut microbiome, leading to various diseases, such as periodontitis, asthma, chronic obstructive pulmonary disease, Crohn’s disease, ulcerative colitis and cancers. However, the exact causal relationship between smoking and microbiome alteration remains to be further explored.

Allergies are characterized by a hypersensitive immune reaction to originally harmless antigens. In recent decades, the incidence of allergic diseases has markedly increased, especially in developed countries. The increase in the frequency of allergic diseases is thought to be primarily due to environmental changes related to a westernized lifestyle, which affects the commensal microbes in the human body. The human gut is the largest organ colonized by bacteria and contains more than 1000 bacterial species, called the “gut microbiota.” The recent development of sequencing technology has enabled researchers to genetically investigate and clarify the diversity of all species of commensal microbes. The collective genomes of commensal microbes are together called the “microbiome.” Although the detailed mechanisms remain unclear, it has been proposed that the microbiota/microbiome, especially that in the gut, impacts the systemic immunity and metabolism, thus affecting the development of various immunological diseases, including allergies. In this review, we summarize the recent findings regarding the importance of the microbiome/microbiota in the development of allergic diseases and also the results of interventional studies using probiotics or prebiotics to prevent allergies.

The rumen microbiome plays a critical role in normal physiology and nutrition of ruminants. Alterations in the rumen microbiome have important physiological and pathological implications. The advent of next-generation sequencing technologies and rapid development of computational tools and reference databases provide powerful tools in rumen microbiome studies. Rumen metagenomics enables studies on the collective genetic structure and functional composition of the rumen microbial community in a culture-independent manner and can be simply divided into functional metagenomics and sequencing-based computational metagenomics. Recent progresses in mining the rumen microbial community for novel enzymes, such as fibrolytic enzymes, or other biomolecules for industry and biotechnology applications using functional screening are discussed. Rapid advances in computational metagenomic tools and methods are summarized. Metagenomics has provided novel insights into the structure and function of the rumen microbiome. Recent efforts suggest that the core rumen microbiome consists of 8 phyla and 15 families, which likely contribute to the basic function of the rumen. Systematic investigations of the rumen microbiome, including its viral (virome) and plasmid (plasmidome) fractions, have revealed previously unrecognized biodiversity in the rumen. Resistance and resilience of the rumen microbial community in response to perturbation is also discussed. Moreover, the need for mechanistic models and applications of general ecological theories and principles in rumen metagenomic studies is emphasized.

Nutrient availability is one of the major limiting factors affecting legume production in Africa. With the limited arable land resources, meeting the dietary requirement of the ever-increasing world population becomes a serious challenge. The most frequently deficient nutrient on crop fields is nitrogen (N). Inconvenient increase in prices of chemical nitrogen fertilizers together with the environmental problems associated with their excessive use calls for alternative low-cost and ecologically friendly soil-plant fertilization technologies. Soil microorganisms play significant roles in nutrient mineralization and supply to plant hence promoting plant growth. Soil microbes suppress soilborne plant diseases and destroy environmentally hazardous compounds in soil. Microbial inoculants are agricultural amendments that use microorganisms such as rhizobia and endophytes to promote legume growth. These microbes form symbiotic relationships with the target leguminous plant, and both parts benefit. The structure and function of the plant microbiome are major determinants of plant health and productivity. Microbial inoculants are the potential tools for sustainable agriculture.

Current agricultural practices demand for low-input technologies with an objective to scale down the synthetic fertilizers and pesticides usage in order to enhance the sustainability in food production and restore ecosystem functioning. Regardless of much understanding of the essential role played by the soil microbiome in agriculture, we still have a limited knowledge of the multifarious response of microbial heterogeneity. To explore this covert attribute of soil microbial diversity, there is a need to focus upon the infinite ways by virtue of which soil microbiome helps in sustainable agriculture. There is limited access to highly diverse and dynamic communities of microbiome in soil due to inability of culture techniques in laboratory. With the advent of next-generation sequencing (NGS) techniques and high-throughput analysis, researchers gained new opportunities to investigate undetermined composition of soil microorganisms. Among rapidly growing field of research, the role of metagenomics is crucial in studying uncultured microbes to comprehend the actual microbial diversity and pertinent cooperation, evolution, and functions in diverse environment. Soil microbiologists are putting efforts in analyzing the phylogenetic diversity of soil niches and subsequently attempting to describe the functions of these soil inhabitants at trophic levels for improvement of soil fertility and productivity for the future generation.

Background

The composition of the gut microbiota has recently been associated with health and disease, particularly with obesity. Some studies suggested a higher proportion of Firmicutes and a lower proportion of Bacteroidetes in obese compared to lean people; others found discordant patterns. Most studies, however, focused on Americans or Europeans, giving a limited picture of the gut microbiome. To determine the generality of previous observations and expand our knowledge of the human gut microbiota, it is important to replicate studies in overlooked populations. Thus, we describe here, for the first time, the gut microbiota of Colombian adults via the pyrosequencing of the 16S ribosomal DNA (rDNA), comparing it with results obtained in Americans, Europeans, Japanese and South Koreans, and testing the generality of previous observations concerning changes in Firmicutes and Bacteroidetes with increasing body mass index (BMI).

Results

We found that the composition of the gut microbiota of Colombians was significantly different from that of Americans, Europeans and Asians. The geographic origin of the population explained more variance in the composition of this bacterial community than BMI or gender. Concerning changes in Firmicutes and Bacteroidetes with obesity, in Colombians we found a tendency in Firmicutes to diminish with increasing BMI, whereas no change was observed in Bacteroidetes. A similar result was found in Americans. A more detailed inspection of the Colombian dataset revealed that five fiber-degrading bacteria, including Akkermansia, Dialister, Oscillospira, Ruminococcaceae and Clostridiales, became less abundant in obese subjects.

Conclusion

We contributed data from unstudied Colombians that showed that the geographic origin of the studied population had a greater impact on the composition of the gut microbiota than BMI or gender. Any strategy aiming to modulate or control obesity via manipulation of this bacterial community should consider this effect.

The biotechnology of desert plants is a vast subject. The main applications in this broad field of study comprises of plant tissue culture, genetic engineering, molecular markers and others. Biotechnology applications have the potential to address biodiversity conservation as well as agricultural, medicinal, and environmental issues. There is a need to increase our knowledge of the genetic diversity through the use of molecular genetics and biotechnological approaches in desert plants in the Arabian Gulf region including those in the United Arab Emirates (UAE). This article provides a prospective research for the study of UAE desert plant diversity through DNA fingerprinting as well as understanding the mechanisms of both abiotic stress resistance (including salinity, drought and heat stresses) and biotic stress resistance (including disease and insect resistance). Special attention is given to the desert halophytes and their utilization to alleviate the salinity stress, which is one of the major challenges in agriculture. In addition, symbioses with microorganisms are thought to be hypothesized as important components of desert plant survival under stressful environmental conditions. Thus, factors shaping the diversity and functionality of plant microbiomes in desert ecosystems are also emphasized in this article. It is important to establish a critical mass for biotechnology research and applications while strengthening the channels for collaboration among research/academic institutions in the area of desert plant biotechnology.

Background

The lung microbiome of healthy individuals frequently harbors oral organisms. Despite evidence that microaspiration is commonly associated with smoking-related lung diseases, the effects of lung microbiome enrichment with upper airway taxa on inflammation has not been studied. We hypothesize that the presence of oral microorganisms in the lung microbiome is associated with enhanced pulmonary inflammation. To test this, we sampled bronchoalveolar lavage (BAL) from the lower airways of 29 asymptomatic subjects (nine never-smokers, 14 former-smokers, and six current-smokers). We quantified, amplified, and sequenced 16S rRNA genes from BAL samples by qPCR and 454 sequencing. Pulmonary inflammation was assessed by exhaled nitric oxide (eNO), BAL lymphocytes, and neutrophils.

Results

BAL had lower total 16S than supraglottic samples and higher than saline background. Bacterial communities in the lower airway clustered in two distinct groups that we designated as pneumotypes. The rRNA gene concentration and microbial community of the first pneumotype was similar to that of the saline background. The second pneumotype had higher rRNA gene concentration and higher relative abundance of supraglottic-characteristic taxa (SCT), such as Veillonella and Prevotella, and we called it pneumotype_SCT. Smoking had no effect on pneumotype allocation, α, or β diversity. Pneumotype_SCT was associated with higher BAL lymphocyte-count (P= 0.007), BAL neutrophil-count (P= 0.034), and eNO (P= 0.022).

Conclusion

A pneumotype with high relative abundance of supraglottic-characteristic taxa is associated with enhanced subclinical lung inflammation.

Background

The degree to which host genetic variation can modulate microbial communities in humans remains an open question. Here, we performed a genetic mapping study of the microbiome in two accessible upper airway sites, the nasopharynx and the nasal vestibule, during two seasons in 144 adult members of a founder population of European decent.

Results

We estimated the relative abundances (RAs) of genus level bacteria from 16S rRNA gene sequences and examined associations with 148,653 genetic variants (linkage disequilibrium [LD] r² < 0.5) selected from among all common variants discovered in genome sequences in this population. We identified 37 microbiome quantitative trait loci (mbQTLs) that showed evidence of association with the RAs of 22 genera (q < 0.05) and were enriched for genes in mucosal immunity pathways. The most significant association was between the RA of Dermacoccus (phylum Actinobacteria) and a variant 8 kb upstream of TINCR (rs117042385; p = 1.61 × 10⁻⁸; q = 0.002), a long non-coding RNA that binds to peptidoglycan recognition protein 3 (PGLYRP3) mRNA, a gene encoding a known antimicrobial protein. A second association was between a missense variant in PGLYRP4 (rs3006458) and the RA of an unclassified genus of family Micrococcaceae (phylum Actinobacteria) (p = 5.10 × 10⁻⁷; q = 0.032).

Conclusions

Our findings provide evidence of host genetic influences on upper airway microbial composition in humans and implicate mucosal immunity genes in this relationship.

All major biomes on earth contain a multitude of microorganisms; of this, a considerable proportion is shared by fungi in terms of abundance, genetic diversity, biomass and total biospheric DNA. In various ecosystems, fungi exist as pathogens, mutualists and decomposers and are of considerable ecological value as they influence nearly every component of the ecosystem services, viz. protection against pathogens, homeostatic balance, decomposition and other functions. Fungi are, however, functionally redundant in some ecosystems and endemic to certain bioregions. Next-generation sequencing has now uncovered unculturable fungal forms that has transformed our understanding towards their role in unexplored environments; cataloguing their diversity and study of their biogeographical patterns at local and global scale have become simpler. The data generated through advanced molecular approaches have introduced the concept of ‘mycobiome’ which was largely overlooked or considered as an integral yet small component of the ‘microbiome’ until now. In this chapter, we report new information that reveals various deterministic factors that shape fungal communities and their probable role in maintaining human, soil and plant health. Finally, we also discuss how the view of mycobiome has taken an independent shape and has more recently helped understand interkingdom interactions.