Volatile Organic Compounds and Their Roles in Bacteriostasis in Five Conifer Species

In order to make clear the functions of plant volatile organic compounds (VOCs) on bacteriostasis and air decontamination, we analyzed the composition and content of VOCs in Pinus tabulaeformis Carr., P. bungeana Zucc., Sabina chinensis Antoine, Picea koraiensis Nakai, and Cedrus deodara G. Don under near-natural conditions using the thermal-desorption cold trap gas chromatography/mass spectrometer technique. The effects of the VOCs on airborne microorganisms were investigated using the method of natural sedimentation. Results showed that the major VOCs were as follows: limonene, β-pinene, α-pinene,and α-caryophyllene in Pinus tabulaeformis and P. bungeana; limonene, borneol acetate, β-pinene, myrcene,and tricylene in S. chinensis; limonene, α-pinene, myrcene, camphene, and β-pinene in Picea koraiensis;and limonene, 2, (10)-pinene, α-pinene, and myrcene in C. deodara. These VOCs and the corresponding foliar extracts inhibited the growth of bacteria and stimulated the growth of fungi. Experimental data using monomers of the VOCs demonstrated that limonene, β-pinene, and three aldehydes could significantly inhibit bacterial growth, suggesting an inhibitory effect of VOCs on the growth of airborne microorganisms in the five conifer species. The bacteriostasis and air-decontaminating effects of plant VOCs are further discussed in terms of their chemical composition.     

Bacterial microbiome of Coptotermes curvignathus （Isoptera： Rhinotermitidae） reflects the coevolution of species and dietary pattern

Coptotermes curvignathus Holmgren is capable of feeding on living trees. This ability is attributed to their effective digestive system that is furnished by the termite＇s own cellulolytic enzymes and cooperative enzymes produced by their gut microbes. In this study, the identity of an array of diverse microbes residing in the gut of C. curvignathus was revealed by sequencing the near-full-length 16S rRNA genes. A total of 154 bacterial phylotypes were found. The Bacteroidetes was the most abundant phylum and accounted for about 65% of the gut microbial profile. This is followed by Firmicutes, Actinobacteria, Spirochetes, Proteobacteria, TM7, Deferribacteres, Planctomycetes, Ferrucomicrobia, and Termite Group 1. Based on the phylogenetic study, this symbiosis can be a result of long coevolution of gut enterotypes with the phylogenic distribution, strong selection pressure in the gut, and other speculative pressures that determine bacterial biome to follow. The phylogenetic distribution of cloned rRNA genes in the bacterial domain that was considerably different from other termite reflects the strong selection pressures in the gut where a proportional composition of gut microbiome of C. curvignathus has established. The selection pressures could be linked to the unique diet preference of C. curvignathus that profoundly feeds on living trees. The delicate gut microbiome composition may provide available nutrients to the host as well as potential protection against opportunistic pathogen.     

Microbial diversity in coastal sediments during pre- and post-tsunami periods in the south east coast of India

Sediment samples were collected from 12 beaches affected by the 2004 Asian Tsunami in the south-east coast of India between Vanagiri and Nagoor. The objective of the present study is to delineate the microbial diversity in pre- and post-tsunami disaster coastal sediments. The collected marine sediments indicate that the overall microbial diversity is higher in the pre-tsunami sediments. The increase in pathogenic bacteria and fungal species after the tsunami is obscured due to inundation and backwashing of seawater along the coast. The reduction of other microbial diversity after the tsunami is attributed that the coastal and shelf sediments play an important role in the demineralization of organic matter, which supports the growth of microbes. The continuous exchange of ocean water and backwashing of coastal sediments by the tsunami wave probably reduced the pathogenic bacterial diversity in the sediments.     

Human Pharyngeal Microbiome May Play A Protective Role in Respiratory Tract Infections

The human pharyngeal microbiome, which resides at the juncture of digestive and respiratory tracts, may have an active role in the prevention of respiratory tract infections, similar to the actions of the intestinal microbiome against enteric infections. Recent studies have demonstrated that the pharyngeal microbiome comprises an abundance of bacterial species that interacts with the local epithelial and immune cells, and together, they form a unique micro-ecological system. Most of the microbial species in microbiomes are obligate symbionts constantly adapting to their unique surroundings. Indigenous commensal species are capable of both maintaining dominance and evoking host immune responses to eliminate invading species. Temporary damage to the pharyngeal microbiome due to the impaired local epithelia is also considered an important predisposing risk factor for infections. Therefore, reinforcement of microbiome homeostasis to prevent invasion of infection-prone species would provide a novel treatment strategy in addition to antibiotic treatment and vaccination. Hence continued research efforts on evaluating probiotic treatment and developing appropriate procedures are necessary to both prevent and treat respiratory infections.     

Distribution of gamasid mites on small mammals in Yunnan Province, China

An investigation of gamasid mites on the body surface of small mammals was carried out in Yunnan Province of China from 1990 to 2004. The small mammal hosts were captured from 25 counties which represent five geographical subregions, namely Middle Subregion of Hengduan Mountains, Southern Subregion of Hengduan Mountains, Eastern Plateau Subregion of Yunnan, Western Plateau Subregion of Yunnan and Southern Moun- tainous Subregion of Yunnan. The captured 10 803 small mammal hosts belong to nine families, 29 genera and 52 species in four orders （Rodentia, Insectivora, Scandentia and Lagomorpha）. A total of 68 571 gamasid mites were collected from the body surface of the captured small mammal hosts and all the gamasid mites were identified to 10 families, 33 genera and 112 species. This paper lists all the mite species, together with their taxonomic position （genera and families） and their corresponding hosts. Much more mite species were found in the Middle Subregion of Hengduan Mountains than in other geographical subregions. The total individuals of mites and small mammals in the Middle Subregion of Hengduan Mountains are also the most plentiful in the five geographical subregions. Three dominant mite species and three dominant small mammal hosts were determined as the dominant species in the investigated areas of Yunnan Province. The dominant hosts are Rattus flavipectus （which accounts for 34.85% of the total individuals）, Apodemus chevrieri （13.43%） and Rattus norvegicus （10.40%） while the dominant gamasid mite species are Laelaps nuttalli （Hirst, 1915） （27.84%）, Laelaps echidninus （Berlese, 1887） （18.38%） and Laelaps guizhouensis （Gu et Wang, 1981） （14.79%）. The results showed the high species diversity of gamasid mites in Yunnan Province and the uneven distribution feature in different subregions.     

Construction and Analysis of Functional Networks in the Gut Microbiome of Type 2 Diabetes Patients

Although networks of microbial species have been widely used in the analysis of 16S rRNA sequencing data of a microbiome, the construction and analysis of a complete microbial gene network are in general problematic because of the large number of microbial genes in metagenomics studies. To overcome this limitation, we propose to map microbial genes to functional units, includ-ing KEGG orthologous groups and the evolutionary genealogy of genes:Non-supervised Ortholo-gous Groups (eggNOG) orthologous groups, to enable the construction and analysis of a microbial functional network. We devised two statistical methods to infer pairwise relationships between microbial functional units based on a deep sequencing dataset of gut microbiome from type 2 dia-betes (T2D) patients as well as healthy controls. Networks containing such functional units and their significant interactions were constructed subsequently. We conducted a variety of analyses of global properties, local properties, and functional modules in the resulting functional networks. Our data indicate that besides the observations consistent with the current knowledge, this study provides novel biological insights into the gut microbiome associated with T2D.     

Correlation of Gut Microbiome Between ASD Children and Mothers and Potential Biomarkers for Risk Assessment

Variation of maternal gut microbiota may increase the risk of autism spectrum disorders(ASDs) in offspring. Animal studies have indicated that maternal gut microbiota is related to neurodevelopmental abnormalities in mouse offspring, while it is unclear whether there is a correlation between gut microbiota of ASD children and their mothers. We examined the relationships between gut microbiome profiles of ASD children and those of their mothers, and evaluated the clinical discriminatory power of discovered bacterial biomarkers. Gut microbiome was profiled and evaluated by 16S ribosomal RNA gene sequencing in stool samples of 59 mother–child pairs of ASD children and 30 matched mother–child pairs of healthy children. Significant differences were observed in the gut microbiome composition between ASD and healthy children in our Chinese cohort. Several unique bacterial biomarkers, such as Alcaligenaceae and Acinetobacter, were identified. Mothers of ASD children had more Proteobacteria, Alphaproteobacteria, Moraxellaceae, and Acinetobacter than mothers of healthy children. There was a clear correlation between gut microbiome profiles of children and their mothers; however, children with ASD still had unique bacterial biomarkers, such as Alcaligenaceae, Enterobacteriaceae, and Clostridium. Candidate biomarkers discovered in this study had remarkable discriminatory power. The identified patterns of mother–child gut microbiome profiles may be important for assessing risks during the early stage and planning of personalized treatment and prevention of ASD via microbiota modulation.     

Genes important for survival or reproduction in Varroa destructor identified by RNAi

The Varroa mite,(Varroa destructor),is the worst threat to honey bee health worldwide.To explore the possibility of using RNA interference to control this pest, we determined the effects of knocking down various genes on Varroa mite survival and reproduction.Double-stranded RNA (dsRNA)of six candidate genes (Da,Pros26S,RpL8, RpL11,RpPO and RpS13)were synthesized and each injected into Varroa mites,then mite survival and reproduction were assessed.Injection of dsRNA for Da (Daughterless)and Pros26S (Gene for proteasome 26S subunit adenosine triphosphatase)caused a significant reduction in mite survival,with 3.57%±1.94% and 30.03%±11.43% mites surviving at 72 h post-inj ection (hpi),respectively.Control mites injected with green fluorescent protein (GFP)-dsRNA showed survival rates of 81.95%±5.03% and 82.36 ±2.81%,respectively. Injections of dsRNA for four other genes (RpL8,RpL11,RpPO and RpS13)did not affect survival significantly,enabling us to assess their effect on Varroa mite reproduction.The number of female offspring per mite was significantly reduced for mites injected with dsRNA of each of these four genes compared to their GFP-dsRNA controls.Knockdown of the target genes was verified by real-time polymerase chain reaction for two genes important for reproduction (RpL8,RpL11)and one gene important for survival (Pros26S). In conclusion,through RNA interference,we have discovered two genes important for mite survival and four genes important for mite reproduction.These genes could be explored as possible targets for the control of Varroa destructor in the future.     

The effect of Tyrophagus putrescentiae on Fusarium poae transmission and fungal community in stored barley in a laboratory experiment

The effect of Tyrophagus putrescentiae on Fusarium poae transmission and fungal community composition was studied in nonsterile barley grain. The experiments included following treatments： control barley without mites; barley containing l0 or 50 mites without preincubation on E poae （Tpl0 and TpS0）; barley containing 10 or 50 mites after preincubation on E poae （FTp 10 and FTp50）. The number of mites, suc cessful transfer of E poae, and changes in the fungal communities were examined after 21 d of experiment. Increase of deoxynivalenol （DON） content in the barley was chosen as a criterion of successful Epoae transfer. The preincubation of T. putrescentiae on Epoae increased DON level approximately to 800 and 300μg/kg of grain for FTpl0 and FTpS0, respectively. T. putrescentiae population growth in FTpl0 was lower than in Tpl0, while no difference was found between FTp50 and Tp50. Fungal communities were compared by amplification, cloning and sequencing of ITS fragments, and operational taxonomic units （OTU） analysis. The OTU analysis did not support the transfer ofF. poae via mites. From the analyzed clones, only 13 cloned sequences clustered with E poae in an OTU defined at distance level 0.07. The related clones originated from FTpl0, Tpl 0, Tp50 and control treatments, but not from FTp50. However, the presence of E poae in FTp50 was confirmed by PCR amplification with specific primers. The observation may be explained by different effect of mite population density, that is, in the high density, （FTp50 treatment） the fungus was overgrazed, while the lower population density （FTp 10） supported E poae transfer.     

Contribution of Root Respiration to Total Soil Respiration in a Leymus chinensis （Trin.） Tzvel, Grassland of Northeast China

The loss of carbon through root respiration Is an Important component of grassland carbon budgets. However, few data are available concerning the contribution of root respiration to total soil respiration in grasslands in China. We Investigated seasonal variations of soil respiration rate, root blomaaa, microbial blomaaa C and organic C content of the soil In a semi-arid Leymus chinensis （Trin.） Tzvel. grassland of northeast China during the 2002 growing season （from May to September）. The linear regression relationship between soil respiration rate and root blomaaa was used to determine the contribution of root respiration to total soil respiration. Soil respiration rate ranged from 2.5 to 11.9 g C/m^2 per d with the maximum in late June and minimum In September. The microbial blomaaa C and organic C content of the soil ranged from 0.3 to 1.5 g C/m^2 and from 29 to 34 g C/kg respectively. Root blomaaa had two peaks, In early June （1.80 kg/m^2） and mid-August （1.73 kg/m^2）. Root respiration rate peaked In mid-August （6.26 g C/m^2 per d）, whereas microbial respiration rate peaked In late June （7.43 g C/m^2 per d）. We estimated that the contribution of root respiration to total soil respiration during the growing season ranged from 38% to 76%.     

Effects of different land use patterns on nifH genetic diversity of soil nitrogen-fixing microbial communities in Leymus Chinensis steppe

Biological nitrogen fixation through prokaryotic microbe is an important source of nitrogen been input into many natural ecosystems. In this study the active diazotrophic community was investigated in the three treatments of mowed, grazed and enclosed Leymus chinensis steppes in Hulunbeier grassland of Inner Mongolia by using approaches of polymerase chain reaction-denaturing gradient gel electrophoresis (PCR–DGGE) and sequence analysis. The community structure and diversity of the bacterial groups from the different samples was further analyzed by using different techniques, such as statistical analysis and diversity index evaluation of the band patterns etc. The results showed that grazing activity significantly reduced the number of species and quantities of nitrogen-fixing microorganisms, as well as the nifH gene diversity. However, enclosed plots had the lowest diversity of nifH gene. While the highest one found in mowing plots. A total of 30 sequences representing 25 different sequence types were recovered from the DGGE gels after phylogenetic constructions. The results also revealed that most sequences were coming from Alphaproteobacteria of Proteobacteria, and characterized by sequences of members of Rhodobacter, Bradyrhizobium, Mesorhizobium, Rhodopseudomonas, Xanthomonas, Azospirillum, Gluconacetobacter, Methylobacterium and Methylocystis. Symbiotic nitrogen-fixers existed in grazing, mowing and enclosed plots accounted for 21.4%, 47.3% and 31.3% respectively in their dominant nitrogen-fixing bacteria. The result of principal components analysis showed that the influence of different land use patterns on nitrogen-fixing microbial communities composition can be ordered as grazing plots > enclosed plots > mowing plots. Nitrogen-fixing microbial communities in L. chinensis steppe were significantly (P < 0.05) influenced by the levels of nitrate nitrogen, total phosphorus, available phosphorus contents and pH value when canonical correspondence analysis was employed to identify relationship between nifH gene and soil physicochemical factors under different land use patterns. The result obtained from correlation analysis showed that there was a significant (P < 0.05) negative relationship between the nitrate nitrogen and the total phosphorus content, furthermore, the available phosphorus content was strongly correlated (P < 0.01) with the pH value.     

Effects of different land use patterns on nifH genetic diversity of soil nitrogen-fixing microbial communities in Leymus Chinensis steppe

Biological nitrogen fixation through prokaryotic microbe is an important source of nitrogen been input into many natural ecosystems. In this study the active diazotrophic community was investigated in the three treatments of mowed, grazed and enclosed Leymus chinensis steppes in Hulunbeier grassland of Inner Mongolia by using approaches of polymerase chain reaction-denaturing gradient gel electrophoresis (PCR–DGGE) and sequence analysis. The community structure and diversity of the bacterial groups from the different samples was further analyzed by using different techniques, such as statistical analysis and diversity index evaluation of the band patterns etc. The results showed that grazing activity significantly reduced the number of species and quantities of nitrogen-fixing microorganisms, as well as the nifH gene diversity. However, enclosed plots had the lowest diversity of nifH gene. While the highest one found in mowing plots. A total of 30 sequences representing 25 different sequence types were recovered from the DGGE gels after phylogenetic constructions. The results also revealed that most sequences were coming from Alphaproteobacteria of Proteobacteria, and characterized by sequences of members of Rhodobacter, Bradyrhizobium, Mesorhizobium, Rhodopseudomonas, Xanthomonas, Azospirillum, Gluconacetobacter, Methylobacterium and Methylocystis. Symbiotic nitrogen-fixers existed in grazing, mowing and enclosed plots accounted for 21.4%, 47.3% and 31.3% respectively in their dominant nitrogen-fixing bacteria. The result of principal components analysis showed that the influence of different land use patterns on nitrogen-fixing microbial communities composition can be ordered as grazing plots > enclosed plots > mowing plots. Nitrogen-fixing microbial communities in L. chinensis steppe were significantly (P < 0.05) influenced by the levels of nitrate nitrogen, total phosphorus, available phosphorus contents and pH value when canonical correspondence analysis was employed to identify relationship between nifH gene and soil physicochemical factors under different land use patterns. The result obtained from correlation analysis showed that there was a significant (P < 0.05) negative relationship between the nitrate nitrogen and the total phosphorus content, furthermore, the available phosphorus content was strongly correlated (P < 0.01) with the pH value.     

Volatile Organic Compounds and Their Roles in Bacteriostasis in Five Conifer Species

In order to make clear the functions of plant volatile organic compounds (VOCs) on bacteriostasis and air decontamination, we analyzed the composition and content of VOCs in Pinus tabulaeformis Carr., P. bungeana Zucc., Sabina chinensis Antoine, Picea koraiensis Nakai, and Cedrus deodara G. Don under near-natural conditions using the thermal-desorption cold trap gas chromatography/mass spectrometer technique. The effects of the VOCs on airborne microorganisms were investigated using the method of natural sedimentation. Results showed that the major VOCs were as follows: limonene, β-pinene, α-pinene,and α-caryophyllene in Pinus tabulaeformis and P. bungeana; limonene, borneol acetate, β-pinene, myrcene, and tricylene in S. chinensis; limonene, α-pinene, myrcene, camphene, and β-pinene in Picea koraiensis; and limonene, 2, (10)-pinene, α-pinene, and myrcene in C. deodara. These VOCs and the corresponding foliar extracts inhibited the growth of bacteria and stimulated the growth of fungi. Experimental data using monomers of the VOCs demonstrated that limonene, β-pinene, and three aldehydes could significantly inhibit bacterial growth, suggesting an inhibitory effect of VOCs on the growth of airborne microorganisms in the five conifer species. The bacteriostasis and air-decontaminating effects of plant VOCs are further discussed in terms of their chemical composition.     

Growth substrates alter aboveground plant microbial and metabolic properties thereby influencing insect herbivore performance

The gut microbiome of plant-eaters is affected by the food they eat, but it is currently unclear how the plant metabolome and microbiome are influenced by the substrate the plant grows in and how this subsequently impacts the feeding behavior and gut microbiomes of insect herbivores. Here, we use Plutella xylostella caterpillars and show that the larvae prefer leaves of cabbage plants growing in a vermiculite substrate to those from plants growing in conventional soil systems. From a plant metab...     

Community structure,dispersal ability and functional profiling of microbiome existing in fat body and ovary of the brown planthopper,Nilaparvata lugens

The endosymbionts play vital roles in growth, development and reproduction in insects. Yeast-like endosymbionts (YLSs) have been well studied in Nilaparvata lugens (N. lugens), but little is known about the tissue-specific bacterial microbiomes, especially on the microbial intersection among internal tissues. Here, the correlation of microbial composition, structure, dispersal ability and functional profiling were illuminated in two tissues, the fat body and ovary in N. lugens. A total of 11 phyla and 105 genera were captured from all samples;Firmicutes and Proteobacteria were the most predominant and accounted for more than 99% in all samples. However, the relative abundance ofFirmicutes and Proteobacteria was significantly different in ovary and fat body through Fisher's Least Significant Difference test. Microbial diversity but not the richness index in the two tissues exhibited significant difference. Furthermore, the microbial community structure of the ovary and fat body were primarily determined by tissue quality. Firmicutes showed strong dispersal ability between ovary and fat body based on the quantitative null model assessing, indicating the frequent interaction of these microbiomes in the two tissues. In addition, the Kyoto Encyclopedia of Genes and Genomes pathways of microbial participation were delineated. The ten most abundant pathways counted for over 46% of the annotation and were shared between the two tissues, mainly containing Energy Metabolism and Amino Acid Metabolism/Biosynthesis. The results will provide insights into the correlation of microbial community structure between ovary and fat body of N. lugens.     

Effects of the long-term application of inorganic fertilizers on microbial community diversity in rice-planting red soil as studied by using PCR-DGGE

The effects of the long-term application of inorganic fertilizers on microbial community diversity were investigated in a rice-planting soil derived from quaternary red clay in the Ecological Experimental Station of Red Soil, Chinese Academy of Sciences. After 13 years' application of different inorganic fertilizers for double rice crops, the community structure of bacteria, archaea, actinomycetes and fungi in the soil changed greatly. The similarity of the SSU rDNA DGGE patterns of these four kinds of microorganisms between the soil without rice-planting and the soil with rice-planting reached only 33% and 66%, respectively. The microbial community structure among treatments with NP, PK and NPK types of P fertilizers were more similar; the similarity of the SSU rDNA DGGE patterns of the four kinds of microorganisms under these treatments reached a high range of 75%–81%. The microbial community structure between the treatment with N and K fertilizers (NK) and the treatment without inorganic fertilization (CK) with the treatments with P fertilizers differed greatly; the similarity of the SSU rDNA DGGE patterns of the four kinds of microorganisms under these treatments reached 69%–77% and 55%–77%, respectively. The results of this study provide a scientific basis for fertilizing and utilizing soil, protecting microbial diversity, and accomplishing the sustainable development of agroecology.     

Effects of the long-term application of inorganic fertilizers on microbial community diversity in rice-planting red soil as studied by using PCR-DGGE

The effects of the long-term application of inorganic fertilizers on microbial community diversity were investigated in a rice-planting soil derived from quaternary red clay in the Ecological Experimental Station of Red Soil, Chinese Academy of Sciences. After 13 years' application of different inorganic fertilizers for double rice crops, the community structure of bacteria, archaea, actinomycetes and fungi in the soil changed greatly. The similarity of the SSU rDNA DGGE patterns of these four kinds of microorganisms between the soil without rice-planting and the soil with rice-planting reached only 33% and 66%, respectively. The microbial community structure among treatments with NP, PK and NPK types of P fertilizers were more similar; the similarity of the SSU rDNA DGGE patterns of the four kinds of microorganisms under these treatments reached a high range of 75%–81%. The microbial community structure between the treatment with N and K fertilizers (NK) and the treatment without inorganic fertilization (CK) with the treatments with P fertilizers differed greatly; the similarity of the SSU rDNA DGGE patterns of the four kinds of microorganisms under these treatments reached 69%–77% and 55%–77%, respectively. The results of this study provide a scientific basis for fertilizing and utilizing soil, protecting microbial diversity, and accomplishing the sustainable development of agroecology.     

Protease expression by microorganisms and its relevance to crucial physiological/pathological events

The treatment of infections caused by fungi and trypanosomatids is difficult due to the eukaryotic nature of these microbial cells,which are similar in several biochemical and genetic aspects to host cells.Aggravating this scenario,very few antifungal and anti-trypanosomatidal agents are in clinical use and,therefore,therapy is limited by drug safety considerations and their narrow spectrum of activity,efficacy and resistance. The search for new bioactive agents against fungi and trypanosomatids has been expanded because progress in biochemistry and molecular biology has led to a better understanding of important and essential pathways in these microorganisms including nutrition,growth, proliferation,signaling,differentiation and death.In this context,proteolytic enzymes produced by these eukaryotic microorganisms are appointed and,in some cases,proven to be excellent targets for searching novel natural and/or synthetic pharmacological compounds,in order to cure or prevent invasive fungal/trypanosomatid diseases.With this task in mind,our research group and others have focused on aspartic-type proteases,since the activity of this class of hydrolytic enzymes is directly implicated in several facets of basic biological processes of both fungal and trypanosomatid cells as well as due to the participation in numerous events of interaction between these microorganisms and host structures.In the present paper,a concise revision of the beneficial effects of aspartic protease inhibitors,with emphasis on the aspartic protease inhibitors used in the anti-human immunodeficiency virus therapy,will be presented and discussed using our experience with the following microbial models:the yeast Candida albicans,the filamentous fungus Fonsecaea pedrosoi and the protozoan trypanosomatid Leishmania amazonensis.     

Microbial Dark Matter: from Discovery to Applications

With the rapid increase of the microbiome samples and sequencing data, more and more knowledge about microbial communities has been gained. However, there is still much more to learn about microbial communities, including billions of novel species and genes, as well as countless spatiotemporal dynamic patterns within the microbial communities, which together form the microbial dark matter. In this work, we summarized the dark matter in microbiome research and reviewed current data mining methods...