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Bacterial symbionts of insects have been shown to play important roles in host fitness. However, little is known about the bacterial community of Tessaratoma papillosa which is one of the most destructive pests of the well-known fruits Litchi chinensis Sonn and Dimocarpus longan Lour in Oriental Region, especially in South-east Asia and adjacent areas. In this study, we surveyed the bacterial community diversity and dynamics of T. papillosa in all developmental stages with both culture-dependent and culture-independent methods by the third-generation sequencing technology. Five bacterial phyla were identified in seven developmental stages of T. papillosa. Proteobacteria was the dominant phylum and Pantoea was the dominant genus of T. papillosa. The results of alpha and beta diversity analyses showed that egg stage had the most complex bacterial community. Some of different developmental stages showed similarities, which were clustered into three phases: (1) egg stage, (2) early nymph stages (instars 1-3), and (3) late nymph stages (instars 4-5) and adult stage. Functional prediction indicated that the bacterial community played different roles in these three phases. Furthermore, 109 different bacterial strains were isolated and identified from various developmental stages. This study revealed the relationship between the symbiotic bacteria and the development of T. papillosa, and may thus contribute to the biological control techniques of T. papillosa in the future.

In the present study, an effort has been made to elucidate the gut bacterial diversity of twelve species of the family Araneidae under three subfamilies collected from 5 states of India along with their predicted metabolic role in functional metabolism. Further, we also compared the host species phylogeny based on partial cytochrome c oxidase subunit I (COI) sequences with the gut bacteria composition dendrogram to decipher the phylosymbiotic relationships. Analysis revealed the presence of 22 bacterial phyla, 145 families, and 364 genera in the gut, with Proteobacteria, Firmicutes, Actinobacteria, and Deinococcus-Thermus as the highest abundant phyla. Moreover, phylum Bacteriodetes was dominated only in Cyclosa mulmeinensis and Chlamydiae in Neoscona bengalensis. At the genus level, Bacillus, Acinetobacter, Cutibacterium, Pseudomonas, and Staphylococcus were the most dominant genera. Furthermore, the genus Prevotella was observed only in Cyclosa mulmeinensis, and endosymbiont Wolbachia only in Eriovixia laglaizei. The differential abundance analysis (DeSeq2) revealed the 19 significant ASVs represented by the genera like Acinetobacter, Vagoccoccus, Prevotella, Staphylococcus, Curvibacter, Corynebacterium, Paracoccus, Streptococcus, Microbacterium, and Pseudocitrobacter. The inter- and intra-subfamilies comparison based on diversity indices (alpha and beta diversity) revealed that the subfamily Araneinae have high richness and diversity than Argiopinae and Gasteracanthinae. The phylosymbiotic analysis revealed that there is no congruence between the gut bacteria composition dendrogram with their host phylogeny.

Small bowel adenocarcinoma (SBA) is a rare malignancy with a poor prognosis and limited treatment options. Despite prior studies, molecular characterization of this disease is not well defined, and little is known regarding Chinese SBA patients. In this study, we conducted multigene next‐generation sequencing and 16S ribosomal RNA gene sequencing on samples from 76 Chinese patients with surgically resected primary SBA. Compared with colorectal cancer and Western SBA cohorts, a distinctive genomic profile was revealed in Chinese SBA cohorts. According to the levels of clinical actionability to targetable alterations stratified by OncoKB system, 75% of patients harbored targetable alterations, of which ERBB2, BRCA1/2, and C‐KIT mutations were the most common targets of highest‐level actionable alterations. In DNA mismatch repair–proficient (pMMR) patients, significant associations between high tumor mutational burden and specific genetic alterations were identified. Moreover, KRAS mutations/TP53 wild‐type/nondisruptive mutations (KRASmut/TP53wt/non‐dis ) were independently associated with an inferior recurrence‐free survival (hazard ratio [HR] = 4.21, 95% confidence interval [CI] = 1.94‐9.14, P, Molecular characterization of small bowel adenocarcinoma (SBA) is not well defined, and little is known regarding Chinese SBA patients. Compared with colorectal cancer and Western SBA cohorts, a distinctive genomic profile was revealed in Chinese SBA cohorts. A molecular subtype of KRAS mutations/TP53 wild‐type/nondisruptive mutations was found to be associated with an inferior recurrence‐free survival in SBA.

This study was conducted over 10 years using an open top chamber experiment in the Sanjiang Plain to explore the impact of environmental parameters and bacterial community composition and structure under long-term conditions of elevated CO2 concentrations (eCO2, 550 μmol·mol−1). Illumina sequencing of 16S rRNA was used to determine soil bacterial communities over the long-term in the Sanjiang Plain. Vegetation characteristics and soil properties were also investigated. Dominant bacterial group was Proteobacteria, accounting for 23.52–39.03%, while there were remarkable changes in the bacterial community composition. eCO2 increased the relative abundance of Subgroup_6 and decreased those of AD3 and Candidatus_Udaeobacter. These variations might be related to gene functions. A redundancy analysis indicated that there was a strong relationship between dominant bacterial phyla and environmental factors (photosynthetic rate, aboveground biomass and stomatal conductance). Structural equation model (SEM) showed that eCO2 and year both affected the soil bacterial community. In contrast, the short-term had greater impacts on the bacterial community under eCO2 compared with the long-term via indirect effects on vegetation and soil characteristics. eCO2 affect soil bacterial community through indirect effects on soil nutrient content and vegetation characteristics in the short-term whereas showed adaptability to eCO2 in the long term.

The gastric microbiota in Crohn’s disease (CD) has not been studied. The purpose of the study was to evaluate differences of stomach microbiota between CD patients and controls. DNA was extracted from gastric mucosal and fluid samples, from 24 CD patients and 19 controls. 16S rRNA gene sequencing identified 1511 operational taxonomic units (OTUs), of which 239 passed the low abundance and low variance filters. All but one CD patients were HP negative. Fifteen bacterial phyla were identified in at least one mucosal or fluid site. Of these, Bacteroidota and Firmicutes accounted for 70% of all phyla. Proteobacteria, Actinobacteriota, and Fusobacteriota combined accounted for 27%. There was significant difference in the relative abundance of Bacteroidota, Proteobacteria, Fusobacteriota, and Campilobacterota between CD patients and controls only in gastric corpus samples. In gastric liquid, there was a significant difference only in Actinobacteriota. Pairwise comparison identified 67 differentially abundant OTUs in at least one site. Of these, 13 were present in more than one comparison, and four differentiating OTUs (Neisseriaceae, Neisseria, Absconditabacteriales, and Microbacteriaceae) were identified at all tested sites. The results reveal significant changes in gastric microbial profiles (beta diversity, phylum, and individual taxa levels) between H. pylori-negative CD patients and controls.

Microorganisms are sensitive to changes in the external environment and are often used as indicators to monitor and reflect water quality. Using Illumina MiSeq sequencing, the characteristics of the microbial community in Shihou Lake water at different time points were analyzed and the key environmental factors affecting the bacterial community were identified. The microbial community diversity in Shihou Lake water was rich and showed significant differences over time. The main bacterial phyla were the Cyanobacteria, Proteobacteria, Actinobacteria, Verrucomicrobia, Bacteroidetes, Chloroflexi, Planctomycetes, Firmicutes, Chlorobi, WS6 and Saccharibacteria. The relative abundance of these major phyla in the sample accounted for 97.83%–99.07% of the total abundance; Cyanobacteria had the highest relative abundance, accounting for 13.07%–44.61% of the total, and the abundance of each dominant phylum was significantly different at different time points. The Shannon and Simpson indexes showed that the diversity of each month was as follows: August > October > July > September > November. The Chao1 and Ace indexes indicated that the order of richness was: November > October > July > August > September. Beta diversity analysis found significant differences in the samples from month to month. Environmental factors such as temperature, total nitrogen, chlorophyll-a, permanganate index, nitrite, pH and ammonia nitrogen had significant effects on microbial community structure.

We studied the microbial communities associated with the Baikal ostracods, Candona sp. (Candonidae). Bacterial biofilms were identified on the shell valves of the ostracods localized near epibiotic ciliates of the genus Lagenophrys (Ciliophora: Lagenoprydae). In situ hybridization confirmed the presence of eubacterial cells in different parts of the ostracod’s body. Bacteria of two morphotypes were detected in bacterial biofilms, including filamentous bacteria. Next-generation sequencing of 16S rRNA bacterial gene fragment allowed us to identify representatives of five bacterial phyla. Members of the phyla Proteobacteria and Bacteroidetes typical of non-marine epibiotic associations of ostracods were dominant taxa in the ostracod microbiomes. Members of other taxa (Actinobacteria, Gracilibacteria and Cyanobacteria) are likely facultative and consumed by ostracods together with detritus. In the ostracod microbiome, a significant proportion (20% of all reads) belonged to the sequences of the genus Rickettsia related to intracellular parasites.

Hot springs harbour diverse and interesting groups of microorganisms adapted to extreme conditions. However, due to limitations in the culture-dependent approach, most of such thermophiles remain uncultured and unexplored. Hence, this study was conducted to gain a comprehensive understanding of the bacterial diversity of Mahapelessa hot spring, Sri Lanka using both culture-dependent and culture-independent approaches. The in situ temperature of the water sample was 44.5 °C and the pH was 8.14. 16S rRNA Sanger sequencing of DNA extracted from the 18 bacterial isolates revealed the presence of eight genera belonging to two phyla: Proteobacteria (84%) and Firmicutes (16%) and the most abundant genus being Klebsiella. A total of 23 bacterial phyla representing 80 classes, 43 orders, 123 families, 205 genera and 83 species were detected by 16S rRNA V3-V4 region by amplicon metagenome sequencing of DNA extracted from water samples, where the most abundant phylum was the Proteobacteria (57.39%), followed by Firmicutes (23.7%) and Chloroflexi (4.14%). The three phyla Actinobacteria, Planctomycetes and Bacteroidetes were also detected less than 3% in abundance while 4.48% of bacteria could not be fit into any known phylum. The most abundant genera were Burkholderia (14.87%), Desulfotomaculum (7.23%) and Stenotrophomonas (6.1%). Four strictly anaerobic bacteria, Anaerosolibacter carboniphilus (0.71%), Bellilinea caldifistulae (0.04%), Salimesophilobacter vulgaris (0.1%), Anaerobacterium chartisolvens (0.12%); two potential plant growth-promoting bacteria, Azospirillum halopraeferens (0.04%) and Bradyrhizobium liaoningense (0.16%) and one potential alkali tolerant and sulphate-reducing bacterium, Desulfovibrio alkalitolerans (0.45%) were recorded. Pigmentiphaga sp. was isolated from Mahapelessa hot spring and to the best of our knowledge, this is the first record of this genus from a hot spring. This study gives insight into the vast bacterial diversity present in the Mahapelessa hot spring from the culture-independent approach which could not be identified using standard culturing techniques.

BackgroundFibrillar adhesins are long multidomain proteins attached at the cell surface and composed of at least one adhesive domain and multiple tandemly repeated domains, which build an elongated stalk that projects the adhesive domain beyond the bacterial cell surface. They are an important yet understudied class of proteins that mediate interactions of bacteria with their environment. This study aims to characterize fibrillar adhesins in a wide range of bacterial phyla and to identify new fibrillar adhesin-like proteins to improve our understanding of host-bacteria interactions.ResultsBy careful search for fibrillar adhesins in the literature and by computational analysis we identified 75 stalk domains and 24 adhesive domains. Based on the presence of these domains in the UniProt Reference Proteomes database, we identified and analysed 3,388 fibrillar adhesin-like proteins across species of the most common bacterial phyla. We found that the bacterial proteomes with the highest fraction of fibrillar adhesins include several known pathogens. We further enumerate the adhesive and stalk domain combinations found in nature and demonstrate that fibrillar adhesins have complex and variable domain architectures, which differ across species. By analysing the domain architecture of fibrillar adhesins we show that in Gram positive bacteria adhesive domains are mostly positioned at the N-terminus of the protein with the cell surface anchor at the C-terminus, while their positions are more variable in Gram negative bacteria. We provide an open repository of fibrillar adhesin-like proteins and domains to facilitate downstream studies of this class of bacterial surface proteins.ConclusionThis study provides a domain-based characterization of fibrillar adhesins and demonstrates that they are widely found across the main bacterial phyla. We have discovered numerous novel fibrillar adhesins and improved the understanding of how pathogens might adhere to and subsequently invade into host cells.

Summary Deep‐sea hydrothermal vents harbour diverse and abundant animals and their symbiotic microorganisms, which together comprise holobionts. The interplay between bacterial members of holobionts and their viruses (phages) is important for maintaining these symbiotic systems; however, phage–bacterium interactions in deep‐sea vent holobionts are not well understood. Marine sponges serve as good models for such studies and are used to unveil phage–bacterium interplay via metagenomic analysis. In three demosponges from deep‐sea hydrothermal vent fields in the southern Okinawa Trough, the genomes of a diverse array of symbiotic bacteria, including 10 bacterial phyla, were found to lack intact prophages. Genes related to diverse anti‐viral defence systems, for example, the restriction–modification and toxin–antitoxin systems, were abundant in the bacterial communities. We also detected phage genes that could complement or compensate host bacterial metabolism, indicating beneficial roles of phage infection. Our findings provide insight into phage–bacterium interplay in sponges from deep‐sea hydrothermal vents.

Sediment environments harbor a repertoire of microorganisms that contribute to animal health and the microecosystem in aquaculture ecosystems, but their community diversity and the potential factors that control it remain unclear. Here, we applied 16S rRNA gene amplicon sequencing to investigate bacterial diversity and assembly mechanisms in the sediments of shrimp cultural ponds at the mesoscale. Our results showed that sediment bacterial communities contained 10,333 operational taxonomic units (OTUs) but had only 34 core OTUs and that the relative abundances of these core OTUs were significantly correlated with the physicochemical properties of the sediments. Proteobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Acidobacteria, Firmicutes, Actinobacteria, Ignavibacteriae, Spirochaetae and Planctomycetes were the ten most abundant bacterial phyla. Notably, some opportunistic pathogens (e.g. Vibrio and Photobacterium) and potential functional microbes (e.g. Nitrospira, Nitrosomonas, Desulfobulbus and Desulfuromusa) were widely distributed in shrimp cultural pond sediments. More importantly, we found that there was a significant negative but weak distance-decay relationship among bacterial communities in shrimp culture pond sediments at the mesoscale, and that the spatial turnover of these bacterial communities appeared to be largely driven by stochastic processes. Additionally, environmental factors, such as pH and total nitrogen, also played important roles in influencing the sediment bacterial structure. Our findings enhance our understanding of microbial ecology in aquatic ecosystems and facilitate sediment microbiota management in aquaculture. KEY POINTS: • Core bacterial taxa in cultural pond sediments contributed to the shrimp health and element cycling. • There was a significant negative distance-decay relationship among bacterial communities in shrimp culture pond sediments at the mesoscale, and its spatial turnover appeared to be largely driven by stochastic processes. • Environmental factors (e.g. pH and total nitrogen) played important roles in influencing bacterial structure in shrimp cultural pond sediments.

In Xinjiang, China, traditional handmade cheese is made from fresh milk under natural environmental conditions and is a common fermented dairy product in the region. Due to differences in production methods between regions, the research conducted on the bacterial diversity of traditional handmade cheese is not comprehensive. Hence, little is known about the relationship between bacteria and cheese quality. Therefore, in this study, cheese samples from Tarbagatay Prefecture, Xinjiang, were chosen for investigation. The bacteria in 17 cheese samples were analyzed by sequencing 16S rRNA using Illumina MiSeq technology. The results showed that there were two dominant bacterial phyla and six dominant bacterial genera in the cheeses. Of these, Lactobacillus and Lactococcus displayed the most significant positive correlation with cheese quality. This study provides data to support the improvement of traditional cheese quality via microbial diversity and lays a foundation for the industrialization of traditional cheese production., Traditional cheese of Xinjiang, China, has a long history and the consumption demand is also increasing. In recent years, people pay more and more attention to the quality and microbial diversity of Xinjiang traditional cheese, which also contains a variety of microbial resources. The results showed that the bacteria in Xinjiang traditional cheese were rich and diverse, and the core dominant genera were Lactobacillus, Streptococcus, Lactococcus, Staphylococcus, Enterococcus, and Acetobacters. This study provides a basis for the industrialization of traditional fermented dairy products.

The attached green alga Cladophora known to harbor microbiota that play important roles in ecosystem, is one of the most common freshwater filamentous green algae in rivers globally, including those in the northern part of Thailand. These rivers mostly run through agricultural regions where herbicides are heavily used to improve crop quality and quantity. The extensively-used herbicide atrazine persists in soil sediments through transport by surface runoff to rivers. The effect of such herbicide contamination on Cladophora microbiota in Thailand have not been investigated. To acquire this information, 16S rDNA amplicons were used to compare microbiota of Cladophora sp. cultures treated with a spectrum of atrazine concentrations. The results showed that the Cladophora microbiome included at least 106 possible Operational taxonomic units (OTUs) representing twelve bacterial phyla which are Acidobacteria, Actinobacteria, Armatimonadetes, Chloroflexi, Cyanobacteria, Deinococcus-Thermus, Epsilonbacteraeota, Nitrospirae, Patescibacteria, Planctomycetes, Proteobacteria, and WPS-2, representing both core and local algal bacteria. The presence of atrazine was also correlated with changes in richness of bacterial taxa suggesting that these algal epibiotic bacteria were differently affected by atrazine treatments.

Sinapigladioside is a rare isothiocyanate‐bearing natural product from beetle‐associated bacteria (Burkholderia gladioli) that might protect beetle offspring against entomopathogenic fungi. The biosynthetic origin of sinapigladioside has been elusive, and little is known about bacterial isothiocyanate biosynthesis in general. On the basis of stable‐isotope labeling, bioinformatics, and mutagenesis, we identified the sinapigladioside biosynthesis gene cluster in the symbiont and found that an isonitrile synthase plays a key role in the biosynthetic pathway. Genome mining and network analyses indicate that related gene clusters are distributed across various bacterial phyla including producers of both nitriles and isothiocyanates. Our findings support a model for bacterial isothiocyanate biosynthesis by sulfur transfer into isonitrile precursors., Alternative pathways: Genetic analyses and labeling studies provide the first insights into the biosynthesis of the rare isothiocyanate natural product sinapigladioside from beetle‐associated bacteria that might protect the beetle offspring against entomopathogenic fungi. Contrary to known isothiocyanate biosynthetic pathways, sinapigladioside assembly involves an isonitrile synthase.

Aim. To conduct a comparative analysis of the microbiome of biopsies of a tumor and normal intestinal epithelium of patients diagnosed with colorectal cancer and to identify of functional activities of the obtained bacterial isolates that affect the development of the tumor. Methods. The study included 50 patients with malignant neoplasms of the colon: 36 men and 24 women. The mean age of the patients was 64.110.2 years. To analyze the microbiota of the biopsies, DNA samples were obtained from the tissue of the unaffected colon mucosa and tumor of the patients. Bacterial 16S rRNA genes fragments were amplified using bar-coded primer bakt_341f. Metagenomic next-generation sequencing was performed using the MiSeq platform (Illumina, USA). The obtained data were processed by bioinformatic methods using the QIIME package. Recognition of microorganisms depending on the morphotype and gram staining of the microflora was carried out using combination differential media and biochemical tests. Statistical analysis was carried out using Microsoft Excel, Service Pack 2 for Office XP, Statistica 6.0 (StatSoft). A comparative analysis was performed with the Student's t-test and the MannWhitney test in case of unmet conditions of validity. Alpha diversity of bacterial communities was quantified by the Shannon diversity index and the UniFrac distance for beta diversity analysis. Results. In patients with colorectal cancer, 5 bacterial phyla were isolated, the predominant of which were Firmicutes and Bacteroidetes, while the content of Actinobacteria was low. In addition, a higher number of representatives of Fusobacteria was observed in the tumor tissue compared to the tissue of a healthy mucosa, at a distance of 5 centimeters proximal to the tumor. The results of this study indicate that the microbiome of a tumor and a healthy mucosa fundamentally differ from each other not only in morphotype and gram staining but also in antagonistic, hemolytic and ribonucleolytic activities. Conclusion. Colonization of the tumor by dominant aggressive Gram-negative bacteria leads to significant changes in the tumor microbiome composition compared with normal mucosa, whose representatives are displaced from the damaged epithelium by more aggressive strains.

Asthma is a chronic inflammatory disease affecting the respiratory system. The global incidence of asthma is rising. Clinical and experimental models of asthma clearly indicate that the disease is multifactorial in nature with a wide array of factors contributing to progression and exacerbation, including interactions between immunological markers and the microbial community populating the respiratory tract. In particular, strict hygiene compliance during the early years of life and early exposure to antibiotics are linked to alterations in the biological environment within the airways and to changes in immunological markers, leading to allergies, such as asthma. With the gap in current research knowledge on the various non-bacterial microbial communities in the asthmatic airways, this review summarizes current methods used to assess microbial diversity as well as evidence for the link between microbial alterations and asthma, including changes in the bacterial microbiome, often characterized by the outgrowth of certain bacterial phyla such as proteobacteria and Firmicutes, in addition to disrupted mycobiome, virome, and parasitome. The current review emphasizes the dynamic, context-dependent changes in the microbiome in asthma and the importance of broad-scope analyses, covering a wide range of taxa. In conclusion, the interaction between the resident microbiota and the immune system is essential and significant in modulating the inflammatory responses; however, further investigations are needed to improve our understanding of the risk factors that disrupt the diversity of the microbiome in the different body systems.

The Amoebozoa, a group containing predominantly amoeboid unicellular protists has been shown to play an important ecological role in controlling environmental bacteria. Amoebozoans not only graze bacteria but also serve as a safe niche for bacterial replication and harbor endosymbiotic bacteria including dangerous human pathogens. Despite their importance, only a few lineages of Amoebozoa have been studied in this regard. In this research, we conducted a comprehensive genomic and transcriptomic study with expansive taxon sampling by including representatives from the three known clades of the Amoebozoa. We used culture independent whole culture and single cell genomics/transcriptomics to investigate the association of bacteria with diverse amoebozoans. Relative to current published evidence, we recovered the largest number of bacterial phyla (64) and human pathogen genera (51) associated with the Amoebozoa. Using single cell genomics/transcriptomics we were able to determine up to 24 potential endosymbiotic bacterial phyla, some potentially endosymbionts. This includes the majority of multi-drug resistant pathogens designated as major public health threats. Our study demonstrates amoebozoans are associated with many more phylogenetically diverse bacterial phyla than previously recognized. It also shows that all amoebozoans are capable of harboring far more dangerous human pathogens than presently documented, making them of primal public health concern.

The ongoing biotechnological revolution is rooted in our knowledge of enzymes. However, metagenomics is showing how little we know about Earth's enzyme repertoire. Deep sequencing has revolutionized our view of the tree of life. The genomes of newly‐discovered organisms are replete with novel sequences, emphasizing the trove of enzyme structures and functions waiting to be explored by biochemists. Here, we sought to draw attention to the vastness of the “enzymatic dark matter” within the tree of life by placing enzymological knowledge in the context of phylogeny. We used kinetic parameters from the BRaunschweig ENzyme DAtabase (BRENDA) as our proxy for enzymological knowledge. Mapping 12,677 BRENDA entries onto the phylogenetic tree revealed that 55% of these data were from eukaryotes, even though they are the least diverse part of the tree. At the next taxonomic level, only four of 18 archaeal phyla and 24 of 111 bacterial phyla are represented in the BRENDA dataset. One phylum, the Proteobacteria, accounts for over half of all bacterial entries. Similarly, the supergroup Amorphea, which includes animals and fungi, contains over half the data on eukaryotes. Many major taxonomic groups are notable for their complete absence from BRENDA, including the ultra‐diverse bacterial Candidate Phyla Radiation. At the species level, five mammals (including human) contribute 15% of BRENDA entries. The taxonomic bias in enzymology is strong, but in the era of gene synthesis we now have the tools to address it. Doing so promises to enrich our biochemical understanding of life and uncover powerful new biocatalysts.

Bacterial communities that enrich in high‐temperature Daqu are important for the Chinese maotai‐flavor liquor brewing process. However, the bacterial communities in three different types of high‐temperature Daqu (white Daqu, black Daqu, and yellow Daqu) are still undercharacterized. In this study, the bacterial diversity of three different types of high‐temperature Daqu was investigated using Illumina MiSeq high‐throughput sequencing. The bacterial community of high‐temperature Daqu is mainly composed of thermophilic bacteria, and seven bacterial phyla along with 262 bacterial genera were identified in all 30 high‐temperature Daqu samples. Firmicutes, Actinobacteria, Proteobacteria, and Acidobacteria were the dominant bacterial phyla in high‐temperature Daqu samples, while Thermoactinomyces, Staphylococcus, Lentibacillus, Bacillus, Kroppenstedtia, Saccharopolyspora, Streptomyces, and Brevibacterium were the dominant bacterial genera. The bacterial community structure of three different types of high‐temperature Daqu was significantly different (p, Thermoactinomyces, Staphylococcus, Lentibacillus, Bacillus, Kroppenstedtia, Saccharopolyspora, Streptomyces, and Brevibacterium were the dominant bacterial genera. Bacterial community structure of white Daqu samples and yellow Daqu samples may be more similar, while that of black Daqu samples differs more from the two. Bacteria from different types of high‐temperature Daqu have similar functions as well as phenotypes, and bacterial metabolism was vigorous in the high‐temperature Daqu.

How the root metabolic profiles and rhizosphere bacterial communities of dioecious plants respond to soil properties and sex identity is largely unknown. In this study, we analyzed root phenolic metabolomes and rhizosphere bacterial microbiomes of Populus euphratica females and males in two P. euphratica plantations with different soil properties to reveal the relative importance of soil and sex effects, and to decipher associations of certain phenolic compounds with specific bacterial taxa. We found that the relative abundances of bacterial OTUs and phenolic metabolites were closely linked to soil properties and sex identity. Soil is the main filter influencing the root phenolic metabolic profiles and rhizosphere bacterial communities of P. euphratica, while sexes and their interactions with soil properties are secondary factors. Differences in the diversity and evenness of phenolic metabolites were affected by plant sex, but not by soil properties. Conversely, the diversity and evenness of bacterial communities were affected by soil properties independent of plant sex. A multiple regression model indicated the presence of associations between root phenolic metabolites and specific soil bacteria taxa. Furthermore, all bacterial phyla and families correlated with at least one phenolic metabolite. Especially, both Nitrosomonadaceae and Cytophagaceae positively correlated with salicylic acid. Thus, our study provides new insights into the ecological mechanism that maintains rhizosphere bacterial communities in P. euphratica plantations in the desert area.

The next generation sequencing (NGS) approach has facilitated the investigations of gut microbiota with high throughput and resolution. The present study was focused on the taxonomic and functional characterization of bacterial community associated with different developmental stages of melon fly, Zeugodacus cucurbitae using 16S ribosomal RNA (rRNA) gene amplicons metagenomics. Z. cucurbitae is considered an invasive and most staid polyphagous pest of cucurbitaceous and other related crops. The taxonomic analysis of highly variable V3–V4 region of bacterial 16S rRNA gene sequencing indicated that the bacterial community associated with Z. cucurbitae consists of a total of 23 bacterial phyla (including unclassified and unassigned bacteria), comprising 32 classes, 69 orders, 99 families and 130 genera. Proteobacteria, Firmicutes, Actinobacteria and Tenericutes were dominant phyla of which family, Enterobacteriaceae was the most abundant in the larval and adult female stages, whereas Mycoplasmataceae was the dominant in the pupal stage. In larval stages of Z. cucurbitae, genus Providencia and Comamonas were the most abundant. However, genus Candidatus-Bacilloplasma and Klebsiella were the most dominant in pupae and adult females of Z. cucurbitae, respectively. PICRUSt analysis conducted for prediction of metabolic activities revealed that associated microbiota were involved in membrane transport, carbohydrate metabolism, amino acid metabolism, energy metabolism, replication and repair processes as well as cellular processes and signalling. The higher number of OTUs was annotated for phosphoglycerate mutase and transketolase in adult females followed by larval stages, which may support the digestive function of the microbiota in larvae and adult females. Our findings provide insights about the high variation in microbiota across developmental stages and basis for microbiota-based management strategies of fruit flies.

The article highlights current research that discusses the importance, role and application potential of endophytic bacteria in industrial horticulture. A review of national and foreign publications on the prevalence, taxonomic composition and function of endophytic bacteria in agricultural and horticultural plant objects is presented. Key endophytic bacterial phyla and genera associated with agricultural plants have been previously characterised. The authors consider the main plant organs and tissues that harbour endophytic bacteria, routes of bacterial colonisation and host-to-host transmission, endophyte relationships with the host species, as well as the genotype, seasonal period, environment, taxonomic and varietal composition of host plants. The host-microbiome relationship is intimate and mutually beneficial. Endophytic bacteria positively impact organogenesis and embryogenesis in agricultural plants, transforming phosphorus and atmospheric nitrogen into plant-absorbable forms and producing hormones that stimulate plant growth. Endophytic flora are able to produce vitamins, siderophores, phytohormones, antibiotic like-substances and phytopathogen-antagonistic exoenzymes, which play a role in enhancing a plant’s resistance to disease and stress, while simultaneously increasing its yield. Current evidence indicates the ability of endophytic bacteria isolated from garden crops to produce indolyl acetic acid, solubilise phosphates, potentially stimulate plant growth and suppress antagonistic phytopathogens. Endophytic bacteria are important regulators of growth, development and fruiting in garden crops, sustaining their reproduction and thus having a strong potential for use in biopreparations in industrial horticulture.

Aspalathus linearis is a commercially important plant species endemic to the Cape Floristic Region of South Africa and is used to produce a herbal tea known as rooibos tea. Symbiotic interactions between A. linearis and soil bacteria play an important role in the survival of Aspalathus plants in the highly nutrient-poor, acidic fynbos soil. The aim of this study was to characterize and compare rhizosphere and bulk soil bacterial communities associated with natural and commercially grown A. linearis, as well as the effect of seasonal changes on these communities. Bacterial communities were characterized using high throughput amplicon sequencing, and their correlations with soil chemical properties were investigated. The N-fixing bacterial community was characterized using terminal restriction fragment length polymorphism and real time quantitative polymerase chain reaction. Actinobacteria, Proteobacteria, and Acidobacteria were the most dominant bacterial phyla detected in this study. Highly similar bacterial communities were associated with natural and commercially grown plants. Significant differences in the bacterial community were observed between rhizosphere and bulk soils collected in the dry season, while no significant differences were detected in the wet season. This study provides insights into bacterial community structure and potential factors shaping bacterial community structure with commercially important A. linearis.

Bacteria play a major role in metabolizing ammonia and other metabolites in recirculating aquaculture systems (RASs). To characterize and compare the bacterial communities in the biofilters of two full-scale RASs for the culture of puffer fish, Takifugu rubripes, at different ages and densities were studied. In overall, 47 807 optimized reads of the 16S rRNA gene with V4–V5 region were obtained from four biofilm samples collected after biofilm maturation. At 97% cut-off level, these sequences were clustered into 500 operational taxonomic units, and were classified into 19 bacterial phyla and 138 genera. At the phylum level, Proteobacteria and Bacteroidetes were the most abundant, followed by Nitrospirae and Planctomycetes. At the genus level, Colwellia, Marinifilum, Oceanospirillum, Lutibacter, Winogradskyella, Pseudoalteromonas, Arcobacter, and Phaeobacter were the top members. Nitrosomonas and Nitrospira were main ammonia- and nitrite-oxidizing bacteria. Differences in bacterial communities at different sampling dates and similarities of both biofilters were revealed in the Venn diagram and cluster analysis. Maintaining a good water quality and health of farmed fish in RASs depended on the correct management of the bacterial communities. This study provides more accurate information on the bacterial communities associated with the bifilters of both RASs.

Objectives The study aimed to examine if the α-diversity and relative abundance of the gastrointestinal bacterial taxa is associated with the response magnitude of markers characteristic of exercise-induced gastrointestinal syndrome in response to exertional-heat stress. Design Cross-sectional. Methods Twenty-two endurance-trained athletes completed 2 h running at 60% V . O2max in hot ambient conditions (35.2 °C, 25% relative humidity). Faecal samples were collected pre-exercise to determine bacterial taxonomy by 16S rRNA amplicon sequencing (Illumina MiSeq platform). Data were processed using the QIIME2 pipeline (v2019.1) establishing taxonomic classification with >95% confidence using SILVA. Pre- and post-exercise blood samples were used to determine plasma I-FABP and cortisol concentrations, and systemic inflammatory response profile. Markers of physiological and thermoregulatory strain, and gastrointestinal symptoms were measured every 10 min during exercise. Associations were determined by partial correlation controlled for body mass variables. Results Positive associations between Tenericutes (r(18) = 0.446, p = 0.049) and Verrucomicrobia (r(18) = 0.450, p = 0.046) phylum, Akkermansiaceae (r(18) = 0.486, p = 0.030) and Ruminococcaceae (r(18) = 0.449, p = 0.047) family and aligned genus groups with I-FABP were observed. Whilst, associations between Faecalibacterium (r(12) = 0.668, p = 0.009) and Ruminoclostridium-9 (r(12) = −0.577, p = 0.031) genus with systemic inflammatory profile were observed. Association between bacterial phyla, family, and genus groups were also observed for gastrointestinal symptoms and markers of thermoregulatory strain (r(18) >0.400, p Conclusions The relative abundance of several commensal bacterial groups showed modest favourable (i.e., low perturbations) or detrimental associations with the magnitude of gastrointestinal integrity perturbations and symptoms, and potentially influences body temperature change, in response to exertional-heat stress.

Rhazya stricta is an important medicinal plant used as native herbal drug to cure various diseases across Asia. Plant-microbe interactions represented by different environment abiotic stress factors that shows effects also on the host plants or on the associated microbial communities. Soil microorganism can be adapted to specific stress conditions and evolve tolerance to this stress. The adjustment of the plant microbiome can productively improve the yield production of essential crops. In the present study, metagenomics analysis of bacterial communities associated with five desert plants (Rhazya stricta, Enneapogon desvauxii, Citrullus colocynthis, Senna italica, and Zygophyllum simplex) was used to highlights the bacterial diversity in the communities of these desert plants, as they also have an importance as folkloric medicinal plants, in addition to their important roles in the ecological and agricultural applications. The results of the bacterial community’s taxonomy showed eleven phyla in each sample, and the most abundant were highlighted for further analysis as it was unassigned phyla. Results indicated that the most commonlyknownphylawere; Actinobacteria, Proteobacteria, Chloroflexi, Firmicutes, Acidobacteria, Gemmatimonadetes, and Bacteroidetes. Further bioinformatics and functional analysis of bacteria are needed to investigate their effectiveness in promoting plant growth and understanding symbiotic relationships under drought-stress conditions, meanwhile, introducing the pinpointed ones in this study will help in achieving this task.

Tanneries are an important industrial sector in Ethiopia; consequently, gaps in wastewater treatment process performance need to be identified as the country increases its emphasis on compliance. A case study was conducted to evaluate physicochemical and microbial water quality at a tannery near Addis Ababa. The treatment process was designed for the following: sulfide oxidation; biological oxygen demand reduction; and chromium removal. While some of Ethiopia's standards for industrial wastewater treatment were met through treatment, effluent COD, sulfide, total nitrogen, and total chromium guidelines were not. 16S rRNA gene analysis was used to evaluate the microbial community composition across the treatment train. The results show that common ruminant phyla were dominant throughout, with Firmicutes and Bacteroidetes comprising 77% to 82% relative abundance. The Firmicutes Clostridium increased consistently in relative abundance with treatment, comprising 39% to 61% of the total bacterial community in the effluent. Improved treatment is needed to meet environmental and public health goals. Practitioner Points Case Study of tannery wastewater treatment in Ethiopia shows ineffective treatment of chemical pollutants.Microbiological pollutants from tannery wastewater systems can introduce agents of importance to public healthThe microbiological composition of tannery influent, mixed liquor and effluent contains mostly four bacterial phyla lead by Firmicutes.Most pathogenic bacterial genera found in the tannery wastewater treatment system became a decreasing percentage of the total population. Clostridium comprises up to 61% of the effluent bacterial population and deserves further evaluation to better understand the consequences of its dominance., Chemical and microbiological characteristics across a tannery wastewater treatment system in Ethiopia

Respiratory microbiome is an understudied area of research compared to other microbiomes of the human body. The respiratory tract is exposed to an array of environmental pollutants, including microbes. Yet, we know very little about the relationship between environmental and respiratory microbiome. The primary aim of our study was to compare the mycobiomes and bacteriomes between three sample types from the same participants, including home dust, saliva, and sputum. Samples were collected from 40 adolescents in a longitudinal cohort. We analyzed the samples using 16s bacterial rDNA and ITS fungal rDNA gene sequencing, as well as quantitative PCR with universal fungal and bacterial primers. Results showed that home dust had the greatest alpha diversity between the three sample types for both bacteria and fungi. Dust had the highest total fungal load and the lowest total bacterial load. Sputum had greater bacterial diversity than saliva, but saliva had greater fungal diversity than sputum. The distribution of major bacterial phyla differed between all sample types. However, the distribution of major fungal classes differed only between sputum and saliva. Future research should examine the biological significance of the taxa found in each sample type based on microbial ecology and associations with health effects.

Biogeographic patterns in soil bacterial communities and their responses to environmental variables are well established, yet little is known about how different types of agricultural land use affect bacterial communities at large spatial scales. We report the variation in bacterial community structures in greenhouse, orchard, paddy, and upland soils collected from 853 sites across the Republic of Korea using 16S rRNA gene pyrosequencing analysis. Bacterial diversities and community structures were significantly differentiated by agricultural land-use types. Paddy soils, which are intentionally flooded for several months during rice cultivation, had the highest bacterial richness and diversity, with low community variation. Soil chemical properties were dependent on agricultural management practices and correlated with variation in bacterial communities in different types of agricultural land use, while the effects of spatial components were little. Firmicutes, Chloroflexi, and Acidobacteria were enriched in greenhouse, paddy, and orchard soils, respectively. Members of these bacterial phyla are indicator taxa that are relatively abundant in specific agricultural land-use types. A relatively large number of taxa were associated with the microbial network of paddy soils with multiple modules, while the microbial network of orchard and upland soils had fewer taxa with close mutual interactions. These results suggest that anthropogenic agricultural management can create soil disturbances that determine bacterial community structures, specific bacterial taxa, and their relationships with soil chemical parameters. These quantitative changes can be used as potential biological indicators for monitoring the impact of agricultural management on the soil environment.

Chronic kidney disease (CKD) of unknown etiology (CKDu) mostly affects agricultural communities in Central America, South Asia, Africa, but likely also in North America and Australia. One such area with increased CKDu prevalence is the Medawachchiya District Secretariat Division of the Anuradhapura District in the North Central Province of Sri Lanka. Recent research has focused on the presence of various microbial pathogens in drinking water as potential causal or contributing factors to CKDu, yet no study to date has performed a more comprehensive microbial and water chemistry assessment of household wells used for domestic water supply in areas of high CKDu prevalence. In this study, we describe the chemical composition and total microbial content in 30 domestic household wells in the Medawachchiya District Secretariat Division. While the chemical composition in the tested wells mostly lies within standard drinking water limits, except for high levels of fluoride (F), magnesium (Mg), sodium (Na), chloride (Cl) and calcium (Ca) in some samples, we find a frequent presence of cyanotoxin-producing Microcystis, confirming earlier studies in Sri Lanka. Since the total microbial content of drinking water also directly influences the composition of the human gut microbiome, it can be considered an important determinant of health. Several bacterial phyla were previously reported in the gut microbiome of patients with CKD. Using these bacteria phyla to define operational taxonomic units, we found that these bacteria also occur in the microbiome of the sampled well water. Based on available environmental data, our study demonstrates associations between the abundances of these bacteria with geographical distribution, well water temperature and likely fertilizer use in the local surface water catchment area of the individual household wells. Our results reinforce the recommendation that household wells with stagnant or infrequently used water should be purged prior to use for drinking water, bathing and irrigation. The latter is suggested because of the reported potential accumulation of bacterial toxins by agricultural crops. The observation that bacteria previously found in chronic kidney disease patients are also present in household wells requires a more detailed systematic study of both the human gut and drinking water microbiomes in CKDu patients, in relation to disease prevalence and progression.

As the main biological components of the air ecosystem, airborne microorganisms play an important role in ecosystem function, and most existing studies focus on their health and environmental effects, while ignoring ecological effects. In this study, air microbial samples from two sampling points in the coastal city of Qingdao were collected by a large volume air sampler. The Illumina MiSeq and PacBio high-throughput sequencing methods were used to analyze the microbial community structure and diversity of the two sampling points. The results showed that there were significant differences in the number and relative abundances of microorganisms identified by the two platforms, and with the refinement of the sample classification, the differences in the community became increasingly significant. Proteobacteria and Firmicutes were the dominant bacterial phyla among the airborne microorganisms. MiSeq sequencing showed that the relative abundances of unidentified bacteria were as high as 8.03–16.42% in MiSeq sequencing, while they were almost undetected in PacBio sequencing. Based on the different sequencing platforms, Bacilli, Gammaproteobacteria and Alphaproteobacteria could be seen as significant gaps in the two sampling points. Betaproteobacteria showed differences only in the coastal area, while the other 14 classes were differentially abundant in the urban area. Pseudomonas was the main genus in the aerosol, followed by Lactococcus. The relative abundances of bacterial taxa displayed statistically significant differences in the different functional areas. There were more diverse microbes in the urban area than in the coastal area; moreover, the relative abundances of dominant genera showed significant differences, such as Variovorax and Deinococcus.

Background and Purpose: Microbiota is defined as a collection of microorganisms that live in the host's body, which can consist of bacteria, archae, viruses, and other eukaryotes. Microbiota in humans is also found in the skin, lungs, urinary tract, oral cavity, although the digestive tract plays a role in contributing to the highest number of microbiota in humans. The purpose of this article is to provide an overview of the various profiles of the gastrointestinal microbiota in children, adults, various ethnicities and races. Methods: This study uses a narrative review method. The data sources of this study come from literature obtained via the internet in the form of research results from national and international journals in 2010-2020 such as Elsevier, Clinical Key, Pubmed, Biomed Research International, Nature Journal, PLOS Computational Biology, PNAS Journal dan American Society For Microbiology. Results: From several collections of journals related to microbiota, many studies reveal that the two bacterial phyla Firmicutes and Bacteroidetes are found in a higher proportion in humans in general followed by Prevotella, Actinobacteria and Bifidobacterium. Whereas in children the microbiota is more dominated by Bacteroidetes / Bifidobacterium and not a few studies have found Clostridium in children. It is no different from ethnicities and races from other countries in that the findings of general microbiota are almost the same. Various microbiota also can be built from the environment, geography, ethnicity and culture. Conclusion: The variability of the microbiota in the human tract is very diverse, it is related to various factors, namely age, genetics, metabolic, diet, diet, lifestyle, environment, geography, ethnicity, culture and socio-economy.

Acidobacteria are one of the widespread and numerically abundant groups of prokaryotes in soils and peatlands. The functional potential of these microorganisms remains poorly understood due to the limited number of cultured and characterized representatives. Acidisarcina polymorpha SBC82 is the only acidobacterium for which the ability to use chitin as a source of nitrogen and carbon has been experimentally proven. The genome of strain SBC82 encodes six proteins from the GH18 glycoside hydrolase family; each of these proteins can be considered as a representative of an independent subfamily. The present bioinformatics study shows that one of these subfamilies contains an extensive group of hypothetical chitinases from the Acidobacteria. This functional annotation was done based on the close relationship with the experimentally characterized enzyme from the proteobacterium Xylella fastidiosa. As shown by phylogenetic analysis, the studied group of acidobacterial proteins originated due to lateral transfer of the ancestral gene from the Firmicutes. Acidobacteria subsequently served as a source for multiple lateral gene transfers to a number of bacterial phyla, including the Proteobacteria. Analysis of metagenomic datasets revealed a wide distribution of chitinase genes in acidobacteria that inhabit wetlands and permafrost soils of the temperate and subarctic climatic zones.

Isolation and cultivation of microbes from environmental samples have been fundamental and important for species identification and investigating functions and ecology of target microbes. While cultivation and isolation of microbes are not easy, the natural environment can “culture” any endemic microbes, and thus key information for culturing and isolating microbes may be encoded in the natural population dynamics of microbes. In this paper, I present the idea that culturability of microbes may be inferred by quantifying dynamics properties of microbes using nonlinear time series analytical tools. To briefly demonstrate the idea, I analyzed high-frequency, quantitative microbial time series obtained for artificial rice plots established at Kyoto University, Japan. I selected bacterial phyla that included sufficient numbers of microbial taxa, and analyzed 398 microbial taxa using empirical dynamic modeling. The nine phyla analyzed generally followed a similar pattern: many microbial taxa fell into the “Simple” dynamics category, and a small proportion of taxa were categorized in “Simple but nonlinear” or “Nearly random” dynamics categories. The present analysis suggested that many microbes in the study system might be cultivated by modifying a relatively small number of conditions. However, the present idea as well as the result is preliminary and premature, and more precise taxonomic information (i.e., species-level identification) and a culturability dataset will help to validate the idea. If the present idea was found to be valid, a priori evaluation of the culturability of microbes would become possible, which would avoid unnecessary costs (labor, time and money) of attempts to cultivate microbes.