Focus: Microbiome: Unraveling the Dynamics of the Human Vaginal Microbiome

Four Lactobacillus species, namely L. crispatus, L. iners, L. gasseri, and L. jensenii, commonly dominate the vaginal communities of most reproductive-age women. It is unclear why these particular species, and not others, are so prevalent. Historically, estrogen-induced glycogen production by the vaginal epithelium has been proffered as being key to supporting the proliferation of vaginal lactobacilli. However, the ‘fly in the ointment’ (that has been largely ignored) is that the species of Lactobacillus commonly found in the human vagina cannot directly metabolize glycogen. It would appear that this riddle has been solved as studies have demonstrated that vaginal lactobacilli can metabolize the products of glycogen depolymerization by α-amylase, and fortunately, amylase activity is found in vaginal secretions. These amylases are presumed to be host-derived, but we suggest that other bacterial populations in vaginal communities could also be sources of amylase in addition to (or instead of) the host. Here we briefly review what is known about human vaginal bacterial communities and discuss how glycogen-derived resources and resource competition might shape the composition and structure of these communities.     

Focus: Microbiome: Breathing Better Through Bugs: Asthma and the Microbiome

Asthma is a highly heterogeneous disease characterized by inflammation of the airways, which invokes symptoms such as wheeze, dyspnea, and chest tightness. Asthma is the product of multiple interconnected immunological processes and represents a constellation of related, but distinct, disease phenotypes. The prevalence of asthma has more than doubled since the 1980s, and efforts to understand this increase have inspired consideration of the microbiome as a key player in the pathophysiology and regulation of this disease. While recent years have seen an explosion of new research in this area, researchers are only beginning to untangle to mechanisms by which the microbiome may influence asthma. This review will focus on the relationship between the microbiome and the immune system and how this influences development of asthma. This review will also highlight evidence that may point the way toward new therapies and potential cures for this ancient respiratory foe.     

Focus: Microbiome: Human Microbiota and Ophthalmic Disease

The human ocular surface, consisting of the cornea and conjunctiva, is colonized by an expansive, diverse microbial community. Molecular-based methods, such as 16S rRNA sequencing, has allowed for more comprehensive and precise identification of the species composition of the ocular surface microbiota compared to traditional culture-based methods. Evidence suggests that the normal microbiota plays a protective immunological role in preventing the proliferation of pathogenic species and thus, alterations in the homeostatic microbiome may be linked to ophthalmic pathologies. Further investigation of the ocular surface microbiome, as well as the microbiome of other areas of the body such as the oral mucosa and gut, and their role in the pathophysiology of diseases is a significant, emerging field of research, and may someday enable the development of novel probiotic approaches for the treatment and prevention of ophthalmic diseases.     

Focus: Microbiome: The Hoops,Hopes, and Hypes of Human Microbiome Research

Recent developments in sequencing methods and bioinformatics analysis tools have greatly enabled the culture-independent analysis of complex microbial communities associated with environmental samples, plants, and animals. This has led to a spectacular increase in the number of studies on both membership and functionalities of these hitherto invisible worlds, in particular those of the human microbiome. The wide variety in available microbiome tools and platforms can be overwhelming, and making sound conclusions from scientific research can be challenging. Here, I will review 1) the methodological and analytic hoops a good microbiome study has to jump through, including DNA extraction and choice of bioinformatics tools, 2) the hopes this field has generated for diseases such as autism and inflammatory bowel diseases, and 3) some of the hypes that it has created, e.g., by confusing correlation and causation, and the recent pseudoscientific commercialization of microbiome research.     

Focus: Microbiome: Gut Microbiome and Infant Health: Brain-Gut-Microbiota Axis and Host Genetic Factors

The development of the neonatal gut microbiome is influenced by multiple factors, such as delivery mode, feeding, medication use, hospital environment, early life stress, and genetics. The dysbiosis of gut microbiota persists during infancy, especially in high-risk preterm infants who experience lengthy stays in the Neonatal intensive care unit (NICU). Infant microbiome evolutionary trajectory is essentially parallel with the host (infant) neurodevelopmental process and growth. The role of the gut microbiome, the brain-gut signaling system, and its interaction with the host genetics have been shown to be related to both short and long term infant health and bio-behavioral development. The investigation of potential dysbiosis patterns in early childhood is still lacking and few studies have addressed this host-microbiome co-developmental process. Further research spanning a variety of fields of study is needed to focus on the mechanisms of brain-gut-microbiota signaling system and the dynamic host-microbial interaction in the regulation of health, stress and development in human newborns.     

Focus: Microbiome: Integrative Therapies in Anxiety Treatment with Special Emphasis on the Gut Microbiome

Over the past decade, research has shown that diet and gut health affects symptoms expressed in stress related disorders, depression, and anxiety through changes in the gut microbiota. Psycho-behavioral function and somatic health interaction have often been ignored in health care with resulting deficits in treatment quality and outcomes. While mental health care requires the professional training in counseling, psychotherapy and psychiatry, complimentary therapeutic strategies, such as attention to a nutritional and diverse diet and supplementation of probiotic foods, may be integrated alongside psychotherapy treatment models. Development of these alternative strategies is predicated on experimental evidence and diligent research on the biology of stress, fear, anxiety-related behaviors, and the gut-brain connection. This article provides a brief overview on biological markers of anxiety and the expanding nutritional literature relating to brain health and mental disorders. A case study demonstrates an example of a biopsychosocial approach integrating cognitive psychotherapy, dietary changes, and mindfulness activities, in treating symptoms of anxiety. This case study shows a possible treatment protocol to explore the efficacy of targeting the gut-brain-axis that may be used as an impetus for future controlled studies.     

Focus: Microbiome: Metagenomic Assembly: Overview,Challenges and Applications

Advances in sequencing technologies have led to the increased use of high throughput sequencing in characterizing the microbial communities associated with our bodies and our environment. Critical to the analysis of the resulting data are sequence assembly algorithms able to reconstruct genes and organisms from complex mixtures. Metagenomic assembly involves new computational challenges due to the specific characteristics of the metagenomic data. In this survey, we focus on major algorithmic approaches for genome and metagenome assembly, and discuss the new challenges and opportunities afforded by this new field. We also review several applications of metagenome assembly in addressing interesting biological problems.     

Focus: Microbiome: Treating Obesity and Metabolic Syndrome with Fecal Microbiota Transplantation

The worldwide prevalence of metabolic syndrome, which includes obesity and its associated diseases, is rising rapidly. The human gut microbiome is recognized as an independent environmental modulator of host metabolic health and disease. Research in animal models has demonstrated that the gut microbiome has the functional capacity to induce or relieve metabolic syndrome. One way to modify the human gut microbiome is by transplanting fecal matter, which contains an abundance of live microorganisms, from a healthy individual to a diseased one in the hopes of alleviating illness. Here we review recent evidence suggesting efficacy of fecal microbiota transplant (FMT) in animal models and humans for the treatment of obesity and its associated metabolic disorders.     

Focus Issue on Roots: Functional Soil Microbiome: Belowground Solutions to an Aboveground Problem

There is considerable evidence in the literature that beneficial rhizospheric microbes can alter plant morphology, enhance plant growth, and increase mineral content. Of late, there is a surge to understand the impact of the microbiome on plant health. Recent research shows the utilization of novel sequencing techniques to identify the microbiome in model systems such as Arabidopsis (Arabidopsis thaliana) and maize (Zea mays). However, it is not known how the community of microbes identified may play a role to improve plant health and fitness. There are very few detailed studies with isolated beneficial microbes showing the importance of the functional microbiome in plant fitness and disease protection. Some recent work on the cultivated microbiome in rice (Oryza sativa) shows that a wide diversity of bacterial species is associated with the roots of field-grown rice plants. However, the biological significance and potential effects of the microbiome on the host plants are completely unknown. Work performed with isolated strains showed various genetic pathways that are involved in the recognition of host-specific factors that play roles in beneficial host-microbe interactions. The composition of the microbiome in plants is dynamic and controlled by multiple factors. In the case of the rhizosphere, temperature, pH, and the presence of chemical signals from bacteria, plants, and nematodes all shape the environment and influence which organisms will flourish. This provides a basis for plants and their microbiomes to selectively associate with one another. This Update addresses the importance of the functional microbiome to identify phenotypes that may provide a sustainable and effective strategy to increase crop yield and food security.In recent years, the term plant microbiome has received substantial attention, since it influences both plant health and productivity. The plant microbiome encompasses the diverse functional gene pool, originating from viruses, prokaryotes, and eukaryotes, associated with various habitats of a plant host. Such plant habitats range from the whole organism (individual plants) to specific organs (e.g. roots, leaves, shoots, flowers, and seeds, including zones of interaction between roots and the surrounding soil, the rhizosphere; Rout and Southworth, 2013). The rhizosphere is the region of the soil being continuously influenced by plant roots through the rhizodeposition of exudates, mucilages, and sloughed cells (Uren, 2001; Bais et al., 2006; Moe, 2013). Thus, plant roots can influence the surrounding soil and inhabiting organisms. Mutually, the rhizosphere organisms can influence the plant by producing regulatory compounds. Thus, the rhizospheric microbiome acts as a highly evolved external functional milieu for plants (for review, see Bais et al., 2006; Badri et al., 2009b; Pineda et al., 2010; Shi et al., 2011; Philippot et al., 2013; Spence and Bais, 2013; Turner et al., 2013a; Spence et al., 2014). In another sense, it is considered as a second genome to a plant (Berendsen et al., 2012). Plant rhizospheric microbiomes have positive or negative influence on plant growth and fitness. It is influenced directly by beneficial mutualistic microbes or pathogens and indirectly through decomposition, nutrient solubilization, nutrient cycling (Glick 1995), secretion of plant growth hormones (Narula et al., 2006; Ortíz-Castro et al., 2008; Ali et al., 2009; Mishra et al., 2009), antagonism of pathogens (Kloepper et al., 2004), and induction of the plant immune system (Pieterse et al., 2001; Ramamoorthy et al., 2001; Vessey, 2003; Rudrappa et al., 2008, 2010). The establishment of plant and rhizospheric microbiome interaction is a highly coordinated event influenced by the plant host and soil. Recent studies show that plant host and developmental stage has a significant influence on shaping the rhizospheric microbiome (Peiffer et al., 2013; Chaparro et al., 2014).There are various factors involved in the establishment of the rhizospheric and endophytic microbiome. They are greatly affected by soil and host type (Bulgarelli et al., 2012; Lundberg et al., 2012). Apart from these factors, other external factors such as biotic/abiotic stress, climatic conditions, and anthropogenic effects also can impact the microbial population dynamics in particular plant species. Plant host species differences can mainly be perceived from the secretory exudates by microbes. The root exudates act as a crucial driving force for multitrophic interactions in the rhizosphere involving microbes, neighboring plants, and nematodes (Bais et al., 2006). Thus, it is important to understand root exudate-shaped microbial community profiling in establishing phenotypes involved in plant health. Microbial components associated with plant hosts have to respond to these exudates along with utilizing them in order to grow competitively in a complex interactive root environment. Commonly, there are three groups of microbes present in the rhizosphere, commensal, beneficial, and pathogenic microbes, and their competition for plant nutrition and interactions confer the overall soil suppressiveness against pathogens and insects (Berendsen et al., 2012).Traditionally, the components of the plant microbiome were characterized by isolating and culturing microbes on different media and growth conditions. These culture-based techniques missed the vast majority of microbial diversity in an environment or in plant-associated habitats, which is now detectable by modern culture-independent molecular techniques for analyzing whole environmental metagenomes (comprising all organisms’ genomes). Over the last 5 years, these culture-independent techniques have dramatically changed our view of the microbial diversity in a particular environment, from which only less than 1% are culturable (Hugenholtz et al., 1998). After discovering the importance of the conserved 16S ribosomal RNA (rRNA) sequence (Woese and Fox, 1977) and the first use of denaturing gradient gel electrophoresis (DGGE) of the amplified 16S rRNA gene in the analysis of a microbial community (Muyzer et al., 1993), there was a sudden explosion of research toward microbial ecology using various molecular fingerprinting techniques. Apart from DGGE, thermal gradient gel electrophoresis, and fluorescence in situ hybridization, clone library construction of microbial community-amplified products and sequencing emerged as other supporting techniques for better understanding of microbial ecology (Muyzer, 1999). Furthermore, there are many newer techniques used to understand the microbiome, from metagenomics to metaproteomics (Friedrich, 2006; Mendes et al., 2011; Knief et al., 2012; Rincon-Florez et al., 2013; Schlaeppi et al., 2014; Yergeau et al., 2014). These techniques cover the whole microbiome, instead of selecting particular species, unlike conventional microbial analysis. However, their presence was not yet correlated well with the phenotypic manifestation (phenome) they establish in the host plant.As a consequence of population growth, food consumption is also increasing. On the other hand, cultivable agricultural land and productivity are significantly reduced due to global industrialization, drought, salinity, and global warming (Gamalero et al., 2009). This problem is only addressed by practicing the sustainable agriculture that protects the health of the ecosystem. The basic principle of sustainable agriculture is to significantly reduce the chemical input, such as fertilizers, insecticides, and herbicides, while reducing the emission of greenhouse gas. Manipulation of the plant microbiome has great potential in reducing the incidence of pests and diseases (van Loon et al., 1998; Kloepper et al., 2004; Van Oosten et al., 2008), promoting plant growth and plant fitness, and increasing productivity (Kloepper and Schroth 1978; Lugtenberg and Kamilova, 2009; Vessey, 2003). Single strains or mixed inoculum treatments induced resistance to multiple plant diseases (Jetiyanon and Kloepper, 2002). In recent years, several microbial biofertilizers and inoculants were formulated, produced, marketed, and successfully used by farmers worldwide (Bhardwaj et al., 2014). Although plants are being considered as a metaorganism (East, 2013), our understanding of the exact manifestation of this microbiome on plant health in terms of phenotypes is insufficient. Of late, there is a surge to understand and explore the genomic wealth of rhizosphere microbes. Hence, this Update will focus mainly on existing knowledge based on the root microbiome, its functional importance, and its potential relationship to the establishment of a host phenome, toward achieving sustainable agriculture.     

Focus: Microbiome: The Impact of the Gut Microbiota on Drug Metabolism and Clinical Outcome

The significance of the gut microbiota as a determinant of drug pharmacokinetics and accordingly therapeutic response is of increasing importance with the advent of modern medicines characterised by low solubility and/or permeability, or modified-release. These physicochemical properties and release kinetics prolong drug residence times within the gastrointestinal tract, wherein biotransformation by commensal microbes can occur. As the evidence base in support of this supplementary metabolic “organ” expands, novel opportunities to engineer the microbiota for clinical benefit have emerged. This review provides an overview of microbe-mediated alteration of drug pharmacokinetics, with particular emphasis on studies demonstrating proof of concept in vivo. Additionally, recent advances in modulating the microbiota to improve clinical response to therapeutics are explored.     

Focus: Microbiome: The Influence of the Gut Microbiota on Host Physiology: In Pursuit of Mechanisms

The results generated from the NIH funded Human Microbiome Project (HMP) are necessarily tied to the overall mission of the agency, which is to foster scientific discoveries as a basis for protecting and improving health. The investment in the HMP phase 1 accomplished many of its goals including the preliminary characterization of the human microbiome and the identification of links between microbiome diversity and disease states. Going forward, the next step in these studies must involve the identification of the functional molecular elements that mediate the positive influence of a eubiotic microbiome on health and disease. This review will focus on recent advances describing mechanistic events in the intestine elicited by the microbiome. These include symbiotic bacteria-induced activation of redox-dependent cell signaling, the bacterial production of short chain fatty acids and ensuing cellular responses, and the secretion of bacteriocins by bacteria that have anti-microbial activities against potential pathogens.     

Focus: Allergic Diseases and Type II Immunity: Advances in Food Allergy Treatment

Food allergies represent life-threatening diseases which are increasing in prevalence with no definitive treatments currently in place. Current treatments are no more than preventative avoidance and symptom management. Research within the field has focused on therapeutic developments to modify the immune response in allergen-specific and non-specific methods. This review of the advances made in treatments intends to cover methods such as oral immunotherapy, modified food protein vaccines as well as the use of alternative medicine. Thus, this review aims to inform and further extend discussion surrounding the potential clinical applications as well as novel routes for further research into an, as of yet, unsolved question.     

Breastmilk-Saliva Interactions Boost Innate Immunity by Regulating the Oral Microbiome in Early Infancy

Introduction

Xanthine oxidase (XO) is distributed in mammals largely in the liver and small intestine, but also is highly active in milk where it generates hydrogen peroxide (H₂O₂). Adult human saliva is low in hypoxanthine and xanthine, the substrates of XO, and high in the lactoperoxidase substrate thiocyanate, but saliva of neonates has not been examined.

Results

Median concentrations of hypoxanthine and xanthine in neonatal saliva (27 and 19 μM respectively) were ten-fold higher than in adult saliva (2.1 and 1.7 μM). Fresh breastmilk contained 27.3±12.2 μM H₂O₂ but mixing baby saliva with breastmilk additionally generated >40 μM H₂O₂, sufficient to inhibit growth of the opportunistic pathogens Staphylococcus aureus and Salmonella spp. Oral peroxidase activity in neonatal saliva was variable but low (median 7 U/L, range 2–449) compared to adults (620 U/L, 48–1348), while peroxidase substrate thiocyanate in neonatal saliva was surprisingly high. Baby but not adult saliva also contained nucleosides and nucleobases that encouraged growth of the commensal bacteria Lactobacillus, but inhibited opportunistic pathogens; these nucleosides/bases may also promote growth of immature gut cells. Transition from neonatal to adult saliva pattern occurred during the weaning period. A survey of saliva from domesticated mammals revealed wide variation in nucleoside/base patterns.

Discussion and Conclusion

During breast-feeding, baby saliva reacts with breastmilk to produce reactive oxygen species, while simultaneously providing growth-promoting nucleotide precursors. Milk thus plays more than a simply nutritional role in mammals, interacting with infant saliva to produce a potent combination of stimulatory and inhibitory metabolites that regulate early oral–and hence gut–microbiota. Consequently, milk-saliva mixing appears to represent unique biochemical synergism which boosts early innate immunity.