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Members of the phylum Planctomycetes colonize a wide range of aquatic and terrestrial habitats, but their functional role in the environment remains poorly understood. One of the suggested roles of these bacteria is their participation in degradation of biopolymers of plant and fungal cell walls. The first experimental evidence for the presence of chitin-degrading ability was obtained for Fimbriiglobus ruber SP5T. The genome of this planctomycete encodes the complete set of enzymes required for utilization of chitin, including the chitinase affiliated with the glycoside hydrolase family GH18. Phylogenetic analysis of the chitinase from Fimbriiglobus revealed occurrence of its close homologue in the genome of another planctomycete, Planctomicrobium piriforme Р3Т. Experimental tests performed with the type strain Р3Т and the newly obtained isolate of this species, strain РХ70, confirmed their ability to grow on amorphous chitin as a source of carbon and nitrogen. Activities of the enzymes involved in chitin degradation, which were determined in tests with fluorochrome-labeled chito-oligosaccharides, were exclusively associated with planctomycete cells and were absent from the culture liquid. Further search in the protein database revealed a number of close homologues of these chitinases in other planctomycetes affiliated with different taxonomic groups. Moreover, phylogenetic analysis pointed to planctomycetes as a possible source of multiple horizontal transfers of chitinase genes to other bacterial phyla, as well as to some eukaryotes. Obtaining proofs for chitin-degrading capabilities in Planctomicrobiumpiriforme suggests emendation of the earlier published description of this species and extends the list of planctomycetes with experimentally confirmed chitinolytic potential.

The current study characterized the taxonomic composition of the uterine and vaginal bacterial communities during estrous synchronization up to timed artificial insemination (TAI). Postpartum beef cows (n = 68) were subjected to pre-synchronization step 21 d prior to TAI (day −21), followed by an industry standard 7 Day Co-Synch on day −9 and TAI on day 0. Uterine and vaginal flushes were collected on days −21, −9, and −2 of the protocol and pH was immediately recorded. Pregnancy was determined by transrectal ultrasound on day 30. Bacterial DNA was extracted and sequenced targeting the V1 to V3 hypervariable regions of the 16S rRNA bacterial gene. Results indicated 34 different phyla including 792 different genera present between the uterus and vagina. Many differences in the relative abundance of bacterial phyla and genera occurred between resulting pregnancy statuses and among protocol days (P < 0.05). At day −2, multiple genera were present in >1% abundance of nonpregnant cows but 0.05). Overall, our study indicates bacterial phyla and genera abundances shift over time and may potentially affect fertility by altering the reproductive tract environment.

Abiotic stresses have adverse effects on the plant growth and productivity. Over the last decades, scientists have been intrigued by the fascinating microorganisms that exist in the rhizosphere of plants growing under extreme environments. Members of bacterial phyla Actinobacteria, Proteobacteria, Firmicutes and Bacteroidetes and archaeal phyla Euryarchaeota and Crenarchaeota are found to be more abundant in the rhizosphere of plants growing in extreme environments. Rhizosphere microbiomes enhance plant growth under abiotic stresses by nitrogen fixation, phytohormones production, mineral solubilization, siderophores and HCN production and eliciting plant defense mechanisms against different bacterial and fungal pathogens. Meta-omics techniques such as metagenomics, metatranscriptomics and metaproteomics can also be used to study complex processes involved in microbe-mediated stress alleviation in different plants growing in extreme environments. These approaches generate multi-layered information that can lead to massive outcomes; hence, there are more chances for implementation in this field. This review summarizes the information about the archaeal and bacterial diversity living in the root microbiome of plants growing under extreme conditions. We also described different mechanisms about role of plant growth promoting microorganisms under abiotic stresses and highlighted the applications of meta-omics approaches to explain further advancement in plant–microbe interactions.

Prepared foods have received increasing attention owing to their convenience, rapidness, and ease of processing in a fast-paced life. The bacterial diversity and composition vary among different prepared foods and are closely related to food safety and human health. However, the knowledge on the bacterial community in prepared foods is still limited. In this study, the bacterial diversity in three kinds of prepared foods (meat, aquatic, and dish) available at supermarkets in Beijing was examined by using the high throughput sequencing technology to identify bacterial 16S rRNA genes. Alpha diversity analysis indicated that Proteobacteria and Firmicutes were the predominant bacterial phyla in prepared meat products, which accounted for 35-49% and 42-58% of the total sequences, respectively. Similar results were observed in prepared aquatic products, except salmon, which had a relatively unique bacterial community with Proteobacteria accounting for 90.72%. In prepared dishes, the proportions of Proteobacteria and Firmicutes were about 39-74% and 8-37%, respectively. The predominant bacterial genera detected in all samples within each kind of prepared foods were used to examine the differences in the bacterial community among three kinds of prepared foods. Results showed that the bacterial community in prepared meat products was much more diverse (14 genera) than those in prepared aquatic products (6 genera) and prepared dishes (2 genera). Acinetobacter was detected in all 288 prepared products. The bacterial community structures of prepared meat and aquatic products were more similar compared to those of prepared dishes. On the other hand, in prepared meat products, the bacterial communities of the samples with the same materials or brands were more similar, and further, among the sample with the same brands, the bacterial communities of the samples from the development zone were clearly different from those of the samples from the main urban area. In prepared aquatic products, the bacterial communities of the samples from the same region were also more similar. In prepared dish products, the bacterial communities of the samples with the same foodstuff or cooking style were more similar. In conclusion, this study revealed that the origin and type of prepared food ingredients, along with the sales location and processing methods, influenced microbial diversity and composition.

Heavy metals are low molecular weight elements which at certain concentrations can cause environmental problems as they accumulate. These metals can be toxic depending on their concentration despite being essential to the metabolism of most organisms. Their accumulation in the environment is mainly due to anthropogenic actions which are difficult to revert. In this context, bacteria have been used to efficiently bioremediate the environment. The aim of this study was to map heavy metal resistant genes from bacterial communities in the Riacho dos Macacos compared to those from Rio Grangeiro, used as the environmental control due to its low heavy metal concentration. The samples were prepared by removing the soil and taking these to a laboratory for DNA extraction and subsequent sequencing using the Illumina Miseq kit. Physico-chemical analysis was also performed to quantify the heavy metal concentration in samples. The data were input in the MG-RAST and analyzed. Various genes associated with copper resistance such as Cu ATPase, multicopper oxidase, czc as well as genes associated with zinc resistance were found, especially from the czc family. In the resistant gene taxonomic analysis, the most common bacterial phyla were Proteobacteria with 49.96% and 59.29%, and Actinobacteria with 23.55 and 12.06% in Riacho dos Macacos and Rio Grangeiro, respectively. Other phyla totaled only 27.63% and 32.12%, respectively.

The endophytic bacterial community of two hyperaccumulators (Arabis alpine, Dysphania ambrosioides) and Veronica ciliate was investigated by Illumina sequencing technology. In addition, the culturable endophytic bacteria (EB) were isolated and their plant-growth promotion capabilities were studied. A dataset consisting of 221,075 filtered high-quality and classifiable unique 16S rDNA gene tags, and an average of 36,846 tags with a mean length of 464-bp for each sample was generated. In total, 10801 different operational taxonomic units (OTUs) were detected, belonging to 18 bacterial phyla, 41 classes, 91 orders, 135 families, and 215 genera. Pseudomonas was the most dominant genus in both shoots and roots of the two hyperaccumulators, making up 81.56% and 81.13%, 41.60% and 77.06% of the total number of OTUs, respectively. However, both Chao 1 and Shannon indices of EB of the two hyperaccumulators were significantly lower than those of V. ciliate (P. 05), except the Shannon index of D. ambrosioides shoots. The endophytic bacterial community of roots and shoots of A. alpine showed greater similarity with that of D. ambrosioides roots (12 km away), and clustered to one group in dendrogram, in clear contrast to that of V. ciliate, which grew closer to A. alpine (60 m away). Combining results of soil and plant analyses, we suggest that the soil properties, especially heavy metal concentration, may influence the plants endophytic bacterial community composition. Pot experiments showed that the strain BXGe71 (Microbacterium sp.) from A. alpine significantly enhanced host plants' growth under multi-heavy metal (HM) stress (P .05, t-test).

Atmospheric ammonia is harmful to poultry and human health. The effect of ammonia on the intestinal microflora of laying ducks is still unknown. In this study, the effects of atmospheric ammonia and exposure time on the intestinal microflora of laying ducks were investigated using 16S rDNA sequencing technology. The body weight, ovary weight, spleen weight, liver weight, and productive performance of laying ducks were also recorded, and the relationship between intestinal microflora diversity and productive performance was analyzed. The results showed that Bacteroidetes, Firmicutes, and Proteobacteria were the dominant bacterial phyla. At the phylum and genus levels, with the exception of the phylum Firmicutes and the genus Sutterella, the top 10 most abundant phyla and genera differed significantly when the ammonia concentration was increased from 10 to 75 ppm and/or the exposure time was extended from 10 to 30 D. Laying rate was highly significantly lower in ducks exposed to 75 ppm ammonia for 10 D compared with those exposed to 10 ppm ammonia for 10 D. Body, ovary, and spleen weights also decreased when the ammonia concentration was increased. At the genus level, Flavonifractor was highly significantly positively correlated with ovary weight. Methanocorpusculum and Anaerotruncus were significantly positively correlated with ovary weight. Lactobacillus was significantly positively correlated with spleen weight. Phascolarctobacterium, Sphaerochaeta, Erysipelotrichaceae_UCG.004, and Lactococcus were significantly positively correlated with spleen weight. These results indicated that ammonia affected the diversity of the intestinal microbiota and the productive performance of laying ducks. Several intestinal microbiota genera were also correlated with organ weights.

Zeugodacus cucurbitae (Coquillet) is one of the most significant and widespread tephritid pest species of agricultural crops. This study reports the bacterial communities associated with Z. cucurbitae from three geographical regions in Southeast Asia (Thailand, Peninsular Malaysia, and Sarawak). The bacterial microbiota were investigated by targeted 16S rRNA gene (V3–V4 region) sequencing using the Illumina Mi-Seq platform. At 97% similarity and filtering at 0.001%, there were seven bacterial phyla and unassigned bacteria, comprising 11 classes, 23 orders, 39 families and 67 genera. The bacterial diversity and richness varied within and among the samples from the three geographical regions. Five phyla were detected for the Sarawak sample, and six each for the Thailand and Peninsular Malaysia samples. Four phyla—Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria—were represented in all the fruit fly specimens, forming the core members of the bacterial community. Proteobacteria was the predominant phylum, followed by Bacteroidetes, Firmicutes, and Actinobacteria. Fifty-three genera were represented in the Thailand sample, 56 in the Peninsular Malaysia sample, and 55 in the Sarawak sample. Forty-two genera were present in all the three geographical regions. The predominant core members were order Enterobacteriales (Proeteobacteria), and family Enterobacteriaceae (Enterobacteriales). Klebsiella (Enterobacteriaceae) was the predominant genus and K. oxytoca the predominant species with all specimens having > 10% relative abundance. The results indicate the presence of a great diversity as well as core members of the bacterial community associated with different populations of Z. cucurbitae.

To study the correlation between root microbiome and its community structure and the health, survival, and growth of its host which is the key to solve the problem of the diversity relationship between wild plants and root microorganism. In this study, we used high-throughput techniques of next generation sequencing (NGS) which was applied to study the endophytic and rhizosphere bacterial and fungal community in hulless barley (Hordeum vulgare) plants, by assessing its PCR amplicon of 16S rDNA sequences and ITS region. The results of the principal component analysis (PCA) showed that bacterial phyla Proteobacteria, Actinobacteria, and Acidobacteria dominate the bacterial community and that the phyla of Ascomycota and Basidiomycota dominate the mycobiota community in the root-soil interface of hulless barley. In both 16S and ITS data, the alpha diversity in bulk soil samples was significantly higher than that of rhizosphere and root samples, and root sample was least diverse, suggesting the microbial selection from the plant host. Beta diversity analysis indicated a clear separation from samples with different sample types (bulk soil, rhizosphere, and root samples). Lastly, the overall microbiota profile and differentially presented taxa were studied to assess the function. It can be concluded that the microbial diversity of wild hulless barley in different soil samples was significantly different and related to host genotypes.

The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf of Mexico. Shotgun metagenomic analysis reveals that each sediment harbors diverse communities of chemoheterotrophs and chemolithotrophs. We recovered 82 metagenome-assembled genomes affiliated with 21 different archaeal and bacterial phyla. Multiple genomes encode enzymes for anaerobic oxidation of aliphatic and aromatic compounds, including those of candidate phyla Aerophobetes, Aminicenantes, TA06 and Bathyarchaeota. Microbial interactions are predicted to be driven by acetate and molecular hydrogen. These findings are supported by sediment geochemistry, metabolomics, and thermodynamic modelling. Overall, we infer that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally diverse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism., Little is known about the microbial ecology of the deep seabed. Here, Dong et al. predict metabolic capabilities and microbial interactions in deep seabed petroleum seeps using shotgun metagenomics, sediment geochemistry, metabolomics, and thermodynamic modelling.

We used Illumina high-throughput sequencing of PCR-amplified V3-V4 16S rRNA gene regions to characterize bacterial communities associated with the adductor muscles, gills, gonads and intestines of the Yesso scallop (Patinopecten yessoensis) from waters around Zhangzidao, Dalian, China. Overall, 421,276 optimized reads were classified as 25 described bacterial phyla and 308 genera. Firmicutes, Proteobacteria, Tenericutes, Bacteroidetes, Chlamydiae and Spirochaetae accounted for > 97% of the total reads in the four organs. The bacterial 16S rDNA sequences assigned to Firmicutes and Proteobacteria were abundant in the adductor muscles, gills and gonads; while reads from Tenericutes were dominant in the intestines, followed by those from Firmicutes, Chlamydiae, Proteobacteria and Bacteroidetes. At the genus level, the dominant genera in the adductor muscles, gills and gonads appeared to be Bacillus, Enterococcus and Lactococcus, whereas Mycoplasma was dominant in the intestines. The relative abundances of Bacillus, Enterococcus, Lactococcus, Alkaliphilus, Raoultella, Paenibacillus and Oceanobacillus were significantly lower in the intestine than in the other three organs. Cluster analysis and principal coordinates analysis of the operational taxonomy units profile revealed significant differences in the bacterial community structure between the intestine and the other three organs. Taken together, these results suggest that scallops have intestine-specific bacterial communities and the adductor muscles, gills and gonads harbor similar communities. The difference in the bacterial community between organs may relate to unique habitats, surroundings, diet and their respective physiological functions.

The increasing of urbanization will lead the increasing violence-related death, like traffic accident, murdered and suicide which contribute to 20 leading causes of death. Post mortem interval (PMI) estimation is important information for suspicious death. Microbes have important role for decomposition of bodies. By evaluate the certain bacteria will know the post mortem interval because the community of bacteria have certain condition regarding to the composition. The aim of this study is to figure out the community of Firmicutes, Actinobacteria and Gammaproteobacteria from rectal swab post mortem interval of the terrestrial environment in Malang, East Java, Indonesia. We used Wistar carcass as a model for human decomposition. Identification of bacterial phyla using Real Time PCR (qPCR) method after cultured in nutrient broth solution. The results showed that Firmicutes has dominant composition in fresh stage (0-24 hours) and in advance decomposition at 120 hours after death. Actinobacteria was dominant in the early decomposition, observed from the 48 to 72 hours after death. While Gammaproteobacteria was dominant in the end of fresh stage and early decomposition stage when bloating time occur.

Gut microbiomes have profound effects on the health of hosts. About 28% of extant parrot species are threatened with extinction. To inform conservation efforts, we characterized and compared the gut microbiomes in nine species of parrots in captivity. The core gut microbiome of parrots was dominated by three bacterial phyla: the Firmicutes, Proteobacteria, and Actinobacteria. This core gut microbiome is similar to that in other herbivorous birds. There were no statistical differences in the diversity of gut microbiomes among parrot species, but significant variations in richness were detected. Individuals of the same species had more similar gut microbial composition to each other than to other species, indicating the potential role of host ancestry on shaping gut microbiomes. However, gut microbiomes did not cluster according to host species. Furthermore, Lactobacillus might influence the gut microbial composition of parrots. These results can contribute to improving our understanding of the basic characteristics of parrot gut microbiomes and help with their conservation.

Wijayanti M, Wahyudi AT, Yuhana M, Engelhaupt M, Meryandini A. 2019. Impact of Bukit Dua Belas rainforest transformation to oil palm plantation on phylogenetic of soil bacterial communities in Sarolangun, Jambi, Sumatra, Indonesia. Biodiversitas 20: 811-818. Land use change from forest to oil palm plantation at Sumatra could decrease biodiversity, including bacterial diversity. The case of Bukit Dua Belas transformation from forest to oil palm plantation was gotten for measuring shift community of soil bacterial in both areas. The diversity of bacterial communities from rainforest and oil palm plantation topsoil in Sumatra was studied using pyrosequencing of 16S rRNA gene and common biodiversity indices. Phylogenetic approach was used to reveal the community shift of bacterial phyla and genera in both areas. Ecological approach was carried out by measuring soil pH, TC (total carbon), TN (total nitrogen), AP (available phosphorous), bacterial diversity with Shannon and Simpson indices, and bacterial richness with Chao1-ACE index and OTUs. Bacterial diversity and richness on lowland forest topsoil and oil palm plantation soil were not different, as soil pH, TC, and TN as substrate factors were not different significantly. The majority of sequences related to Acidobacteria (56.33%), Proteobacteria (27.43%), Actinobacteria (7.11%), and Cyanobacteria (5.55%) were from forest; whereas those related to Acidobacteria (50.11%), Proteobacteria (31.63%), Actinobacteria (7.58%), Chloroflexi (2.60%), and Gemmatimonadetes (2.71%) invented from oil palm plantation. Acidobacteria was the most dominant phyla in both habitats, because soil pH in both areas was acidic (3.77 - 4.80 pHH2O). The genera of alpha-proteobacteria dominated in genera phylotype of bacterial 16S rRNA phylogenetic revealed in both forest and oil palm plantation topsoil. The most genera in phylogenetic tree are Burkholderia from Beta-proteobacteria. The bacterial community shift occurred in forest transformation, even though the oil palm plantation showed more bacterial phyla and genera than the lowland rainforest.

Heavy metals (HM) contamination in soils due to anthropogenic activities is a serious environmental problem. In this study, we investigated the impact of Pb, Cd and Zn at soil pollution levels on soil organisms, with special attentions to microbiota. We monitored by Illumina MiSeq technology and bioinformatics analysis the functional and structural evolution of the HM-exposed soil microbiome after different exposure times (0–160 days). Ecotoxicological tests showed 100% acute toxicity of HMs towards the nematode Caenorhabditis elegans and a significant decrease in the metabolic activity of bacteria. Firmicutes was the most resistant phylum, which selectively displaced other bacterial phyla (Proteobacteria, Actinobacteria and Verrucomicrobia). This was likely related to its capability to form endospores under stressed environment. A bioinformatics analysis using PICRUSt showed that HM exposure had a strong effect on metabolic pathways, specifically, genetic information processing (transcription factors), metabolism (glycan biosynthesis and energy metabolism), and environmental information processing (transporters and ABC transporters), particularly after 55 days of exposure. The assessment of functional and structural development of a HM-exposed soil allowed evaluation on the cellular adaptive responses to the tested environmental stresses, and provided valuable information to assist developing effective remediation strategies of HMs polluted soils using bacteria as the remediator.

Koumiss is notable for its nutritional functions, and microorganisms in koumiss determine its versatility. In this study, the bacterial and fungal community structures in traditional koumiss from Inner Mongolia, China, were investigated. Our results demonstrated that 6 bacterial phyla represented by 126 genera and 49 species and 3 fungal phyla represented by 59 genera and 57 species were detected in 11 samples of artisanal koumiss. Among them, Lactobacillus was the predominant genus of bacterium, and Kluyveromyces and Saccharomyces dominated at the fungal genus level. In addition, there were no differences in the bacterial and fungal richness and diversity of koumiss from 3 neighboring administrative divisions in Inner Mongolia, and the bacterial and fungal community structures (the varieties and relative abundance of bacterial and fungal genera and species) were clearly distinct in individual samples. This study provides a comprehensive understanding of the bacterial and fungal population profiles and the predominant genus and species, which would be beneficial for screening, isolation, and culture of potential probiotics to simulate traditional fermentation of koumiss for industrial and standardized production in the future.

Compared to drinking water, the higher bacterial abundance, diversity, and organic matter concentration in reclaimed wastewater suggest that it is more likely to form biofilms. Nevertheless, little is known regarding many important aspects of the biofilm ecology in reclaimed wastewater distribution systems (RWDS), such as the long-term microbial community succession and the underlying driving factors. In the present study, by sampling and analysing microbial compositions of pipe wall biofilms from six frequently used pipe materials under NaClOdisinfection (sodium hypochlorite-treated), NONdisinfection (without disinfection), and UVdisinfection (UV-treated) treatments over one year, it was found that the succession of microbial community structure followed a primary succession pattern. This primary succession pattern was reflected as increases in live cell number and α-diversity, along with metagenic succession in taxonomic composition. Proteobacteria, Nitrospirae, Bacteroidetes, Acidobacteria, Planctomycetes, Actinobacteria, and Verrucomicrobia comprised the dominant phyla in biofilm samples. Compared to biofilms in the NaClOdisinfection reactor, the bacterial communities of biofilms in NONdisinfection and UVdisinfection reactors were distributed more evenly among different bacterial phyla. Principal component analysis revealed a clear temporal pattern of microbial community structures in six kinds of pipe wall biofilms albeit a difference in microbial community structures among the three reactors. Adonis testing indicated that the microbial community composition variation caused by disinfection methods (R2 = 0.283, P

A total of 43 phyla (395 genera) of bacteria and 11 phyla (309 genera) of fungi were identified from normal sapwood (SW), wetwood (WW) and their transition zone wood (TW) in living poplar trees, with bacteria showing significantly higher diversity than fungi. Highly variable community diversities and compositions were found for bacteria but not for fungi among WW, TW and SW. Overall, 22 phyla (95 genera) bacteria and three phyla (11 genera) fungi were significantly different in relative abundance between WW and SW. Nine wood chemical properties were significantly correlated with the relative abundance of top 15 bacterial and fungal genera in all samples. Wetwood represents an abnormal condition of heartwood in living poplar trees. The cause of wetwood formation is still poorly understood, but it is generally considered to involve microbial activities. To facilitate a better understanding of wetwood formation, we sequenced the 16S rRNA and ITS (Internal Transcribed Spacer) genes of distinct regions (16S V4, ITS1) to precisely identify the microbial communities in normal sapwood (SW), wetwood (WW) and their transition zone wood (TW). Nine chemical properties of the wood samples were further determined to elucidate the correlations between the microbial communities and wood characteristics. The total sequences of 16S V4 and ITS1 from WW, TW and SW were assigned to 43 bacterial phyla (395 genera) and 11 fungal phyla (309 genera), indicating a significantly higher diversity of bacteria than fungi. Among SW, TW and WW, significant variations in community diversity and composition were found for bacteria but not for fungi. WW had the highest bacterial and lowest fungal diversities, while SW exhibited the highest fungal diversity. TW generally exhibited intermediate levels between WW and SW. Between WW and SW, 22 bacterial phyla (95 genera) were significantly different in relative abundance. Nine wood chemical properties were significantly correlated with the relative abundance of top 15 bacterial and fungal genera in all wood samples.

Bactrocera carambolae Drew & Hancock is an agricultural pest that causes considerable damage to various fruit crops in Southeast Asia and South America. We report here the bacterial communities associated with field-caught male and female adult flies from University Malaya campus. The microbiota was determined by targeted 16S rRNA gene (V3–V4 region) sequencing using the Illumina MiSeq. At 97% similarity, four bacterial phyla (with relative abundance of ≥1% in at least one specimen) – Bacteroidetes, Firmicutes, Proteobacteria, and Tenericutes – were recovered from the adult flies. Proteobacteria was the predominant phylum in all the samples, with the female flies (86.81 ± 6.57%) having higher mean relative abundance than the male flies (71.57 ± 18.37%). The Firmicutes was more abundant in the male flies (14.47 ± 17.30%) than female flies (0.69 ± 1.25%). There were in total seven classes, nine orders, 13 families, 23 genera, and 31 putative species. Thirteen genera had higher mean relative abundance in male flies, and nine in female flies. Klebsiella was the predominant genus in female flies, while Desulfovibrio was more abundant in some male flies. The mean relative abundances of the putative species Orbus sasakiae and Enterococcus moraviensis were significantly higher in male than female flies, while female flies had significantly higher mean relative abundance for Escherichia fergusonii and Klebsiella variicola. Alpha diversity indices indicated that the bacterial diversity varied within and between male and female flies, and the mean bacterial diversity was significantly higher in male flies. The differences in bacterial diversity and relative abundance may be reasonably attributed to stochastic processes, in part to environmental factors such as food resources and habitats. It is significant that several putative bacterial species recovered in the present study have not been reported in Bactrocera fruit flies. Sixteen of the 31 detected putative bacterial species are potential opportunistic pathogens of medical/public health importance.

Reference genomes are essential for metagenomic analyses and functional characterization of the human gut microbiota. We present the Culturable Genome Reference (CGR), a collection of 1,520 nonredundant, high-quality draft genomes generated from >6,000 bacteria cultivated from fecal samples of healthy humans. Of the 1,520 genomes, which were chosen to cover all major bacterial phyla and genera in the human gut, 264 are not represented in existing reference genome catalogs. We show that this increase in the number of reference bacterial genomes improves the rate of mapping metagenomic sequencing reads from 50% to >70%, enabling higher-resolution descriptions of the human gut microbiome. We use the CGR genomes to annotate functions of 338 bacterial species, showing the utility of this resource for functional studies. We also carry out a pan-genome analysis of 38 important human gut species, which reveals the diversity and specificity of functional enrichment between their core and dispensable genomes., A resource of >1,500 bacterial reference genomes sheds light on the human gut microbiome.

Soil bacteria play a critical role in the functioning of ecosystems but are challenging to investigate. We developed state-factor models with machine learning to understand better and to predict the abundance of 10 dominant phyla and bacterial diversities in Australian soils, the latter expressed by the Chao and Shannon indices. In the models, we used proxies for the edaphic, climatic, biotic and topographic factors, which included soil properties, environmental variables, and the absorbance at visible–near infrared (vis–NIR) wavelengths. From a cross-validation with all observations (n = 681), we found that our models explained 43–73% of the variance in bacterial phyla abundance and diversity. The vis–NIR spectra, which represent the organic and mineral composition of soil, were prominent drivers of abundance and diversity in the models, as were changes in the soil-water balance, potential evapotranspiration, and soil nutrients. From independent validations, we found that spectro-transfer functions could predict well the phyla Acidobacteria and Actinobacteria ( R 2 > 0.7) as well as other dominant phyla and the Chao and Shannon diversities ( R 2 > 0.5). Predictions of the phyla Firmicutes were the poorest ( R 2 = 0.42). The vis–NIR spectra markedly improved the explanatory power and predictability of the models.

The effects of phosphorus (P) availability on soil microbial community and its functional responses have not been widely explored till date. The present study involved high throughput sequencing of 16S rRNA to investigate the bacterial community structure, size and function in long-term fertilized paddy soils that received P fertilizers (+ P) and compared with soils without P fertilizer (− P) application. Data analysis revealed that changes in P availability in the soil significantly influenced the phylogenetic composition of bacterial communities and their functional profiles. The populations of bacterial phyla Verrucomicrobia, Bacteroidetes, Acidobacteria, Chloroflexi, and Cyanobacteria were significantly induced in (− P) treatment when compared with (+ P). The bacterial genus Geobacter reported to use high-affinity P transporter during P limitation and Massilia known as a prominent P solubilizer were significantly more abundant in (− P) soils. The functional profile analysis demonstrated (− P) soils were characterized by more abundant enzymes related to P cycling. The present study enabled us to characterize the dominant indigenous microbiome of (− P) soils and also provided a better insight into the ecological and evolutionary responses of microbes in P limited soils.

Aims To describe the effects of foliar fertilizer application on the bacterial populations of almond tree leaves. Methods and results We applied a commercially available foliar fertilizer or a water control onto the leaves of almond trees and collected leaves after 1, 7, 14 and 56 days and examined their bacterial populations by 16S rRNA gene sequence analysis. After 1 day, we observed significant differences in 3 of the 4 predominant bacterial phyla, and 5 of the 13 predominant bacterial families. After 7 days, we observed significant differences in all of the predominant phyla, and 8 of the 13 predominant families. After 14 days, the number of significant differences decreased, and after 56 days only 2 of the 13 predominant families differed significantly. Conclusions Foliar fertilization significantly altered the bacterial population structure of almond leaves as compared to the water control. While most of the observed perturbation was transient, significant differences remained after 56 days. Significance and impact of the study This is the first report describing the effects of foliar fertilization on the bacterial populations of almond leaves and provides new insights as to how this process alters the leaf bacterial population structure.

In this study, the accelerated biodegradation of PLA/PHB (polylactic acid/polyhydroxybutyrate)-blended nonwovens was investigated in the presence of a microbial community. The PLA/PHB-blended nonwovens were buried in natural soil for 56 days, with soil samples collected for subsequent bacterial community domestication. The tensile strength and elongation at break of the PLA/PHB-blended nonwovens as well as the CO2 generated by the Gen III and natural soil communities were determined to assess the degradation rates of the polymer samples. After incubation for 15 days with the Gen III soil bacterial suspension, the surfaces and fibrous structure of nonwovens and the fibers within the nonwovens exhibited distinct changes. In addition, the amount of EvCO2 reached 566.79 mg, the tensile strength decreased from 10.95 ± 0.7 to 2.57 ± 0.31 MPa, a loss of 77%, and the elongation at break changed from 5.32 ± 0.45 to 7.07 ± 1.04%. The 16S rRNA pyrosequencing results showed that Proteobacteria and Firmicutes were the 2 most important bacterial phyla in the Gen III community, accounting for 80.4 and 19.4% of the total classified sequences, respectively. The results of this study demonstrate that compared to a natural soil microbial community, the domesticated strains in the Gen III community, especially members of the phyla Proteobacteria and Firmicutes, are useful in accelerating the degradation of PLA/PHB-blended nonwovens.

In China, air pollution has become a significant environmental threat to human health in recent years. Airborne bacteria are critical constituents of microbial aerosols, which contain numerous pathogens. However, the effects of seasonal variations, environmental factors such as air pollution, and meteorological factors on microbial diversity are poorly understood. In this study, fine particulate matter (PM2.5) samples (n = 12) were collected using a high-volume air sampler over 24-hour periods during all four seasons from April 2017 to January 2018. Concurrently, the average daily concentrations of various air pollutants and the meteorological conditions were monitored. High-throughput sequencing of 16s rRNA was then employed to profile PM2.5 bacterial communities. The results showed that the bacterial communities varied significantly by season. Proteobacteria (35.5%), Firmicutes (23.0%), and Actinobacteria (16.2%) were the most abundant bacterial phyla in the PM2.5 samples. At the genus level, the diversity of the bacterial communities was significantly correlated with the ozone (O3) concentration (r = 0.920, p = 0.001) and air temperature (T) (r = 0.534, p = 0.023). The results of this study can be used as a reference by other bioaerosol research that focuses on the health effects of atmospheric particulate matter.

The objectives of this study were to determine the biofilm microbial activity and bacterial community structure and successions in greywater treatment filters and to relate the treatment efficiency to the bacterial community parameters. This 10-month study was performed in a newly established experimental system for domestic greywater treatment that consisted of three parallel vertical flow filters (VFs) followed by a horizontal flow filter (HF). A rapid increase in the bacterial community abundance occurred during the first 85 days of filter operations, followed by a short-term decrease and the stabilization of the 16S rRNA gene copy numbers at average levels of 1.2 × 109 and 3.2 × 108 copies/g dw in VFs and HF, respectively, until the end of the experiment. The dominant bacterial phyla and genera differed between the VFs and HF. The temporal variation in the bacterial community structure was primarily related to the species replacement, and it was significantly affected by the influent organic carbon and nitrogen compounds in the VFs and the ammonia and organic carbon in the HF filters. Despite the differences in the community structure and assembly mechanisms, the temporal dynamics of the bacterial community showed high congruence between the filter types. The treatment efficiency was related to the biofilm bacterial community diversity and abundance and the abundance of certain bacterial genera in the VF filters. The results suggest that the dominant pathway of nitrogen removal by greywater treatment VFs occurs via coupled heterotrophic nitrification and denitrification, while the contribution of aerobic denitrification is temporally variable in these filters.

Organic matter degradation and bacterial communities associated to the thermophilic phase of composting were compared using two different types of anaerobic digestates, one from a sewage sludge digester (SD), and the other from an agricultural digester (AD). The composting process exhibited similar variations in temperature, pH, moisture content and bacterial profiles, despite the inherent feedstock differences along with distinctive initial bacterial composition. According to the data obtained from 16S rRNA gene amplicon sequencing, SD constituted more than 20 bacterial phyla with Proteobacteria (21%) and Chloroflexi (21%) being predominant, meanwhile AD was represented by only 7 phyla in which Firmicutes was the most abundant phylum (73%). Nevertheless, bacterial community profiles of the two composting systems became more similarly represented at the phylum level, both dominated by Proteobacteria (65% in AD and 61% in SD), whereas Chromatiaceae and Sphingomonadaceae were the most abundant families in AD and SD, respectively. Highly diverse but similar bacterial communities were detected during the composting of different anaerobic digestates at the thermophilic phase.

Globitermes sulphureus is a major pest in coconut plantations and also a secondary pest in the urban, suburban and rural areas of building structures, as well as in tropical agriculture areas. Although the literature revealed microbiome in termite guts, the bacterial community in G. sulphureus intestinal tracts remain largely unidentified. Here, we aimed to characterize the bacterial community associated with the worker and soldier castes of G. sulphureus using 16S metagenomic. The Illumina HiSeq 2500 sequencing machine was used to amplify the V3 and V4 regions of the 16S rRNA gene. The sequencing output was analyzed using Qiime pipeline v1.9.1. The result of the analysis showed that Spirochaetes, Fibrobacteres, Firmicutes, Proteobacteria, and Bacteroidetes were the dominant phyla that reside in the guts of the worker and soldier castes. We found that the worker and soldier castes shared similar bacterial phyla in their guts but different bacterial genera. Our findings provided a baseline information on microbial community inhabiting G. sulphureus guts up to the genus level for some phyla.

Rice is an important crop in Uruguay associated mostly with livestock production in a rice and pasture rotation system since the 1920s. However, in recent years there has been interest in intensifying the production in some of these systems to satisfy market demands and increase income. Intensification occurs by augmenting the rice frequency in the rotation, including new crops like sorghum and soybean, or shortening the pasture phase. A long-term experiment was established in 2012 in the main rice producing area of Uruguay with the objective to study the impact of intensification in rice rotations. After the first cycle of rotation soils from seven rotation phases were sampled and microbial communities were studied by means of high-throughput sequencing of Illumina NovaSeq 6000. Archaeal/bacterial and fungal community composition were studied (16S rRNA and 18S gene regions) detecting 3662 and 807 bacterial and fungal Operational Taxonomic Units (OTUs), respectively.Actinobacteria,FirmicutesandProteobacteriawere the most common bacterial phyla. Among them, onlyProteobacteriadiffered significantly between rotations. Although most fungal OTUs were unidentified,Ascomycota,BasidiomycotaandMucoromycotawere the most abundant fungal classes within identified taxa. Bacterial communities differed between rotations forming three groups according to the percentage of rice in the system. Fungal communities clustered in four groups, although not well differentiated, and mostly associated with the antecessor crop. Only P and C:N varied between rotations among soil physicochemical variables after six years, and individual bacterial OTUs appeared weakly influenced by P, pH, Mg and fungal OTUs by P. The results suggest that after six years, bacteria/archaeal communities were influenced by the time with rice in the rotation, and fungal communities were more influenced by the antecessor crop. More studies are needed to associate fungal communities with certain rotational or environmental variables. Some taxa were associated with a particular rotation, and some bacterial taxa were identified as biomarkers. Fungal indicator taxa were not identified at the species level for any rotation.

Bacterial microcompartments (BMCs) are protein-based organelles that expand the metabolic potential of many bacteria by sequestering segments of enzymatic pathways in a selectively permeable protein shell. Sixty-eight different types/subtypes of BMCs have been bioinformatically identified based on the encapsulated enzymes and shell proteins encoded in genomic loci. BMCs are found across bacterial phyla. The organisms that contain them, rather than strictly correlating with specific lineages, tend to reflect the metabolic landscape of the environmental niches they occupy. From our recent comprehensive bioinformatic survey of BMCs found in genome sequence data, we find many in members of the human microbiome. Here we survey the distribution of BMCs in the different biotopes of the human body. Given their amenability to be horizontally transferred and bioengineered they hold promise as metabolic modules that could be used to probiotically alter microbiomes or treat dysbiosis.

This study was conducted to evaluate the ambient water bacterial dynamics and its influence on the gut of resident teleosts; Oreochromis niloticus. The bacterial communities in the ambient water and the gastrointestinal tract (GIT) of O. niloticus were profiled using a culture-dependent method and followed by the 16S rRNA gene sequencing. The results indicated bacterial phyla of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes respectively between the two microbial consortia. However, the relative abundance among the bacterial phyla notably differed between the two consortia. The relative abundance of Proteobacteria (≤ 67%) was dominant in both consortia, but contrarily, Actinobacteria and Bacteroidetes were higher in the ambient water relative to the GIT which indicated Proteobacteria and Bacilli as the highest diversity. Nevertheless, the relative abundance of γ-proteobacteria and Bacilli remarkably dominated both consortia at the class level, with Bacillus and Pseudomonas being the most abundant operational taxonomic units (OTUs).

The ruminant gut microbial community's importance has been widely acknowledged due to its positive roles in physiology, metabolism, and health maintenance. Diarrhea has been demonstrated to cause adverse effects on gastrointestinal health and intestinal microecosystem, but studies regarding diarrheal influence on gut microbiota in Giraffa camelopardalis have been insufficient to date. Here, this study was performed to investigate and compare gut microbial composition and variability between healthy and diarrheic G. camelopardalis. The results showed that the gut microbial community of diarrheal G. camelopardalis displayed a significant decrease in alpha diversity, accompanied by distinct alterations in taxonomic compositions. Bacterial taxonomic analysis indicated that the dominant bacterial phyla (Proteobacteria, Bacteroidetes, and Firmicutes) and genera (Escherichia Shigella and Acinetobacter) of both groups were the same but different in relative abundance. Specifically, the proportion of Proteobacteria in the diarrheal G. camelopardalis was increased as compared with healthy populations, whereas Bacteroidetes, Firmicutes, Tenericutes, and Spirochaetes were significantly decreased. Moreover, the relative abundance of one bacterial genus (Comamonas) dramatically increased in diarrheic G. camelopardalis, whereas the relative richness of 18 bacterial genera decreased compared with healthy populations. Among them, two bacterial genera (Ruminiclostridium_5 and Blautia) cannot be detected in the gut bacterial community of diarrheal G. camelopardalis. In summary, this study demonstrated that diarrhea could significantly change the gut microbial composition and diversity in G. camelopardalis by increasing the proportion of pathogenic to beneficial bacteria. Moreover, this study first characterized the distribution of gut microbial communities in G. camelopardalis with different health states. It contributed to providing a theoretical basis for establishing a prevention and treatment system for G. camelopardalis diarrhea.

Extensive knowledge and methodological expertise on the bacterial cell biology have been accumulated over the last decades and bacterial cells have now become an integral part of several (bio-)technological processes. While it appears reasonable to focus on a relatively small number of fast-growing and genetically easily manipulable model bacteria as biotechnological workhorses, the for the most part untapped diversity of bacteria needs to be explored when it comes to bioprospecting for natural product discovery. Members of the underexplored and evolutionarily deep-branching phylum Planctomycetes have only recently gained increased attention with respect to the production of small molecules with biomedical activities, e.g. as a natural source of novel antibiotics. Next-generation sequencing and metagenomics can provide access to the genomes of uncultivated bacteria from sparsely studied phyla, this, however, should be regarded as an addition rather than a substitute for classical strain isolation approaches. Ten years ago, a large sampling campaign was initiated to isolate planctomycetes from their varied natural habitats and protocols were developed to address complications during cultivation of representative species in the laboratory. The characterisation of approximately 90 novel strains by several research groups in the recent years opened a detailed in silico look into the coding potential of individual members of this phylum. Here, we review the current state of planctomycetal research, focusing on diversity, small molecule production and potential future applications. Although the field developed promising, the time frame of 10 years illustrates that the study of additional promising bacterial phyla as sources for novel small molecules needs to start rather today than tomorrow.

Whole-genome sequences were generated from 96 bacterial strains of 14 species that were isolated from International Space Station surfaces during the Microbial Tracking 2 study. Continued characterization of this closed habitat's microbiome enables tracking of the spread and evolution of secondary pathogens, which is vital for astronaut health.

The last decade saw extensive studies of the human gut microbiome and its relationship to specific diseases, including gallstone disease (GSD). The information about the gut microbiome in GSD-afflicted Russian patients is scarce, despite the increasing GSD incidence worldwide. Although the gut microbiota was described in some GSD cohorts, little is known regarding the gut microbiome before and after cholecystectomy (CCE). By using Illumina MiSeq sequencing of 16S rRNA gene amplicons, we inventoried the fecal bacteriobiome composition and structure in GSD-afflicted females, seeking to reveal associations with age, BMI and some blood biochemistry. Overall, 11 bacterial phyla were identified, containing 916 operational taxonomic units (OTUs). The fecal bacteriobiome was dominated by Firmicutes (66% relative abundance), followed by Bacteroidetes (19%), Actinobacteria (8%) and Proteobacteria (4%) phyla. Most (97%) of the OTUs were minor or rare species with ≤1% relative abundance. Prevotella and Enterocossus were linked to blood bilirubin. Some taxa had differential pre- and post-CCE abundance, despite the very short time (1–3 days) elapsed after CCE. The detailed description of the bacteriobiome in pre-CCE female patients suggests bacterial foci for further research to elucidate the gut microbiota and GSD relationship and has potentially important biological and medical implications regarding gut bacteria involvement in the increased GSD incidence rate in females.

Faecal microbiota transplantation (FMT) has received considerable attention in recent years due to its remarkable efficacy in restoring a normal gut microbiome. Here, we established the groups of post-FMT recipient piglets using germ-free piglets during early life to characterize the colonization of gut microbiota composition and the enrichment of resistance gene acquisition. By metagenomic analysis, we identified 115 bacterial phyla and 2111 bacterial genera that were acquired by the FMT recipients. We found that early-life microbial colonization and the spread of resistomes in recipient piglets were age dependent. A total of 425, 425 and 358 AR genes primarily belonging to 114, 114 and 102 different types were detected in the donors, post-FMT recipients in the FMT-3D group and post-FMT recipients in the FMT-15D group respectively. Genes that encoded tetracycline, macrolide and chloramphenicol resistance proteins were the most dominant AR genes, and the results corresponded with the exposure of antibiotic consumption at farm. Bacteroides, Escherichia, Clostridium, Parabacteroides, Treponema, Lactobacillus and Enterococcus were significantly correlated with the distribution of AR genes. More importantly, the relative abundance of AR genes was positively correlated with the levels of mobile genetic elements. Our results indicate that early-life microbial colonization can persistently shape the gut microbiota and antibiotic resistome.

BackgroundThe microbiome has emerged as an environmental factor contributing to obesity and type 2 diabetes (T2D). While the majority of studies have focused on associations between the gut microbiome and metabolic disease, increasing evidence suggests links between circulating bacterial components (i.e. bacterial DNA) and cardiometabolic disease as well as blunted response to metabolic interventions such as bariatric surgery. In this aspect, thorough next generation sequencing based and contaminant aware approaches are lacking. To address these points, we tested whether bacterial DNA could be amplified in the blood of subjects with obesity and high metabolic risk under strict experimental and analytical control to minimize bacterial contamination. Moreover we characterized a bacterial signature associated with the individual metabolic risk and explored its dynamics alongside metabolic improvement after bariatric surgery.MethodsSubjects undergoing elective bariatric surgery were recruited into sex and BMI matched subgroups with (n=24) or without T2D (n=24). Bacterial DNA in the blood was quantified and prokaryotic 16S rRNA gene amplicons were sequenced. A contaminant aware approach was applied to derive a compositional microbial signature from bacterial sequences in subjects with and without T2D and within subjects at baseline and at three and twelve months post bariatric surgery. We modelled associations between bacterial load and composition with host metabolic and anthropometric markers. We further tested whether compositional shifts were related to weight loss response and T2D remission after bariatric surgery. Lastly, Catalyzed Reporter Deposition (CARD) - Fluorescence In Situ Hybridization (FISH) was employed to visualize bacteria in blood samples.ResultsContaminant aware classification of bacterial 16S rRNA sequences allowed the derivation of a blood bacterial signature, which was associated with metabolic health. Based on bacterial phyla and genera detected in the blood samples, a metabolic syndrome classification index score was derived and shown to robustly classify subjects along their actual clinical group. T2D was characterized by decreased bacterial richness and a loss of genera associated with improved metabolic health. Moreover, circulating bacterial load was significantly associated with metabolic health and increased after bariatric surgery. Weight loss and metabolic improvement following bariatric surgery were associated with an early and stable increase of these genera in parallel with improvements in key cardiometabolic risk parameters. CARD-FISH allowed the detection of living Bacteria in blood samples in obesity.ConclusionsWe show that the circulating bacterial signature reflects metabolic disease and its improvement after bariatric surgery. Our work provides contaminant aware evidence for the presence of living bacteria in the blood and suggests a putative crosstalk between components of the blood and metabolism in metabolic health regulation.

Host-microbe interactions may influence dermatitis pathogenesis in the nasomaxillary folds of French bulldogs, which is often complicated by secondary bacterial and fungal infections.To assess the skin-fold microbiome in systemically healthy French bulldogs and to determine the influence of topical medications on this microbiome.Nineteen healthy French bulldogs.Next-generation DNA sequencing was applied to characterise the microbiome composition in the nasomaxillary folds of systemically healthy French bulldogs. Subsequently, the effect of two topical products on the fold microbiome was assessed. Seven dogs were treated with a protease product (Kalzyme; enzyme) that inhibits biofilm formation without biocidal activity, six dogs were treated with a 2% chlorhexidine diacetate solution (Nolvasan; CHX) with biocidal activity, and six dogs were untreated. Dogs were randomly assigned to each group, and the investigator was blinded.The primary skin bacterial phyla inhabiting the folds at inclusion were Firmicutes, Actinobacteria and Proteobacteria. The primary skin fungal phyla were Ascomycota and Basidiomycota. Topical treatment increased the diversity of bacterial and fungal compositions over time (increase in microbial diversity score: enzyme 38%, chlorhexidine 11%, control5%) and the relative abundance of pathogens reduced significantly (enzyme, P = 0.028; CHX, P = 0.048). A clear correlation (rThe nasomaxillary skin-fold microbiome of healthy French bulldogs contained a high abundance of clinically relevant pathogens (mean 36.4%). Topical therapy with enzyme increased microbial diversity of skin folds and reduced the relative abundance of pathogens.Les interactions hôte-microbe peuvent influencer la pathogénie de la dermatite dans les plis naso-maxillaires du bouledogue français, souvent compliquée par des infections bactériennes et fongiques secondaires.Evaluer le microbiome des plis cutanés chez les bouledogues français sains et déterminer l’influence des médications topiques sur ce microbiome.Dix neuf bouledogues français sains. MATÉRIELS ET MÉTHODES: Le séquençage d’ADN de dernière génération a été appliqué pour caractériser la composition du microbiome des plis naso-maxillaires de bouledogues français sains. L’effet de deux topiques sur le microbiome des plis a été évalué. Sept chiens ont été traités avec protéase (Kalzyme; enzyme) qui inhibe la formation de biofilm sans activité biocide, six chiens étaient non traités. Les chiens ont été répartis au hasard dans chaque groupe et l’investigateur était en aveugle. RÉSULTATS: Les phyla bactériens cutanés primaires inhibant les plis à l’inclusion étaient Firmicutes, Actinobacteria et Proteobacteria. Les phyla fongiques primaires cutanés étaient Ascomycota et Basidiomycota. Le traitement topique a augmenté la diversité des compositions bactériennes et fongiques dans le temps (augmentation du score de diversité microbienne : enzyme 38%, chlorhexidine 11%, contrôle5%) et l’abondance relative des pathogènes a diminué significativement (enzyme, P = 0.028; CHX, P = 0.048). Une corrélation nette (rLe microbiome des plis cutanés naso-maxillaires des bouledogues français sains contient une abondance élevée de pathogènes cliniquement significatifs (moyenne 36,4%). Le traitement topique avec enzyme augmente la diversité microbienne des plis cutanés et réduit l’abondance relative des pathogènes.INTRODUCCIÓN: las interacciones huésped-microbio pueden influir en la patogenia de la dermatitis en los pliegues nasomaxilares de los Bulldogs Franceses, que a menudo se complica por infecciones bacterianas y fúngicas secundarias. OBJETIVO: evaluar el microbioma del pliegue cutáneo en Bulldogs Franceses sistémicamente sanos y determinar la influencia de los medicamentos tópicos en este microbioma. ANIMALES: diecinueve Bulldogs Franceses sistémicamente sanos. MÉTODOS Y MATERIALES: se aplicó la secuenciación de DNA de próxima generación para caracterizar la composición del microbioma en los pliegues nasomaxilares de Bulldogs Franceses sistémicamente sanos. Posteriormente, se evaluó el efecto de dos productos tópicos en el pliegue del microbioma. Siete perros fueron tratados con un producto de proteasa (Kalzyme; enzima) que inhibe la formación de biopelículas sin actividad biocida, seis perros fueron tratados con una solución de diacetato de clorhexidina al 2% (Nolvasan; CHX) con actividad biocida y seis perros no fueron tratados. Los perros se asignaron al azar a cada grupo y el investigador fue cegado. RESULTADOS: los filos de bacterias cutáneas primarias que habitaban los pliegues en el momento de la inclusión fueron Firmicutes, Actinobacteria y Proteobacteria. Los principales filos fúngicos de la piel fueron Ascomycota y Basidiomycota. El tratamiento tópico aumentó la diversidad de composiciones bacterianas y fúngicas con el tiempo (aumento en la puntuación de diversidad microbiana: enzima 38%, clorhexidina 11%, control5%) y la abundancia relativa de patógenos se redujo significativamente (enzima, P = 0,028; CHX, P = 0,048). Se observó una clara correlación (rDie Interaktion von Wirt und Mikroben könnte die Pathogenese der Dermatitis in den nasomaxillären Falten von Französischen Bulldoggen, welche oft durch sekundäre bakterielle Infektionen oder durch Pilzinfektionen verkompliziert wird, beeinflussen. ZIEL: Eine Erfassung des Mikrobioms der Hautfalten bei systemisch gesunden Französischen Bulldoggen und eine Feststellung, welchen Einfluss eine topische Behandlung auf dieses Mikrobiom hat.Neunzehn systemisch gesunde Französische Bulldoggen.Next-Generation DNA-Sequenzierung wurde angewendet, um die Zusammensetzung des Mikrobioms in den nasomaxillären Falten von systemisch gesunden französischen Bulldoggen zu charakterisieren. In der Folge wurde die Auswirkung zweier topisch angewendeter Produkte auf das Mikrobiom der Falten erfasst. Sieben Hunde wurden mit einem Protease Produkt (Kalzyme; Enzym) behandelt, welches ohne eine biozide Wirkung Biofilmbildung verhindert, sechs Hunde wurden mit 2%iger Chlorhexidindiacetatlösung (Nolvasan; CHX) mit biozider Aktivität behandelt und sechs Hunde wurden nicht behandelt. Die Hunde wurden zufällig in die Gruppen eingeteilt, die UntersucherInnen wurden geblindet.Die bakteriellen Primärstämme, die die Falten bewohnten, waren Firmicutes, Actinobacteria und Proteobacteria. Die mykotischen Primärstämme waren Ascomycota und Basidiomycota. Durch die topische Behandlung vergrößerte sich mit der Zeit die Diversität der bakteriellen Zusammensetzung sowie der Zusammensetzung der Pilze (Zunahme des mikrobiellen Diversitätswerts: Enzym 38%, Chlorhexidin 11%, Kontrolle5%) und die relative Häufigkeit der Pathogene war signifikant reduziert (Enzym, P = 0,028; CHX, P = 0,048). Eine deutliche Korrelation (rDie Mikrobiome der nasomaxillären Hautfalten von systemisch gesunden Französischen Bulldoggen beinhalten eine große Anzahl an klinisch relevanten Pathogenen (Durchschnitt 36,4%). Eine topische Therapie mit Enzymen erhöht die mikrobielle Diversität der Hautfalten und reduziert die relative Häufigkeit der Pathogene.背景: フレンチブルドッグの鼻上顎ヒダにおける皮膚炎の病態には、宿主と微生物の相互作用が影響している可能性があり、二次的な細菌や真菌感染を伴うことが多い。 目的: 本研究の目的は、健常フレンチブルドッグの皮膚表面のマイクロバイオームを評価し、このマイクロバイオームに対する外用薬の影響を明らかにすることであった。 供試動物: 19頭の健常フレンチブルドッグ。 材料と方法: 次世代DNAシーケンサーを用いて、健常フレンチブルドッグの鼻上顎ヒダにおけるマイクロバイオームの構成を明らかにした。その後、2種類の外用剤がヒダのマイクロバイオームに及ぼす影響を評価した。7頭の犬には殺菌性のないバイオフィルム形成阻害プロテアーゼ製品 (カルザイム; 酵素) を、6頭の犬には殺菌性のある2%クロルヘキシジンジアセテート溶液 (ノルバサン; CHX) を、6頭の犬には無処置を施した。犬は各グループに無作為に割り当てられ、調査者は盲検化された。 結果: 研究包含時に、ヒダに生息していた主要な皮膚細菌門は、Firmicutes、Actinobacteria、Proteobacteriaであった。また、皮膚の真菌類は、AscomycotaおよびBasidiomycotaであった。外用療法により、細菌および真菌の組成の多様性は時間の経過とともに増加し (微生物多様性スコアの増加: 酵素38%、クロルヘキシジン11%、対照5%未満) 、病原菌の相対的な存在量は有意に減少した (酵素、P = 0.028、CHX、P = 0.048) 。臨床的に重要な病原菌の存在量および微生物の多様性間に明確な相関関係 (r2 = 0.83)を認めた。 結論: 健常フレンチブルドッグの鼻上顎ヒダのマイクロバイオームには、臨床関連病原体が多く含まれていた (平均36.4%) 。酵素を用いた外用療法は、鄒襞部の微生物の多様性を高め、病原菌の相対的な存在感を低下させる。.背景: 宿主-微生物相互作用可能影响法国斗牛犬鼻上颌皱襞皮炎的发生, 通常并发继发性细菌和真菌感染。 目的: 评估全身健康的法国斗牛犬的皮褶微生物组, 并确定外用药物对该微生物组的影响。 动物: 19只全身健康的法国斗牛犬。 方法和材料: 应用新一代DNA给全身健康的法国斗牛犬鼻上颌皱襞微生物组测序, 描述其特征。随后, 评估了两种外用产品对微生物组折叠的影响。7只犬接受抑制生物膜形成而无杀菌活性的蛋白酶产物 (Kalzyme; 酶) 治疗, 6只犬接受具有杀菌活性的2%双乙酸氯己定溶液(Nolvasan;CHX)治疗, 6只犬未接受治疗。将犬随机分配至各组, 并对研究者设盲。 结果: 常驻褶皱处的皮肤细菌门包括厚壁菌门、放线菌门和变形菌门。主要皮肤真菌门包括子囊菌门和担子菌门。随着时间的推移, 外部治疗增加了细菌和真菌组成的多样性 (微生物多样性评分增加: 酶38%, 氯己定11%, 对照5%) , 病原体的相对丰度显著降低 (酶, P = 0.028;CHX,P = 0.048) 。观察到临床相关病原体的丰度与微生物多样性之间存在明确的相关性(r2 = 0.83)。 结论: 全身健康法国斗牛犬的鼻上颌皮褶微生物组含有高丰度的临床相关病原体 (平均36.4%) 。酶外部治疗增加了皮肤皱襞的微生物多样性, 降低了病原体的相对丰度。.As interações entre hospedeiro e microrganismo podem influenciar a patogênese da dermatite na dobra nasomaxilar de buldogues franceses, que é frequentemente complicada por infecções bacterianas e fúngicas secundárias.Avaliar o microbioma de dobras cutâneas em buldogues franceses sistêmicamente saudáveis e determinar a influência de medicações tópicas neste microbioma.Dezenove buldogues franceses sistêmicamente saudáveis. MÉTODOS E MATERIAIS: Sequenciamento de DNA de última geração foi aplicado para caracterizar a composição do microbioma nas dobras nasomaxilares de buldogues franceses sistêmicamente saudáveis. Subsequentemente, o efeito de dois produtos tópicos no microbioma da dobra foi avaliado. Sete cães foram tratados com um produto a base de protease (Kalzyme; enzima) que inibe a formação de biofilme sem atividade biocida, seis cães foram tratados com uma solução de diacetato de clorexidina a 2% (Nolvasan; CHX) com ação biocida, e seis cães não receberam tratamento. Os cães foram aleatoriamente divididos entre os grupos, e o investigador era cego.Os principais filos bacterianos habitantes das dobras cutâneas na inclusão no estudo foram Firmicutes, Actinobateria e Proteobacteria. Os principais filos de fungos foram Ascomycota e Basidiomycota. O tratamento tópico aumentou a diversidade das composições bacterianas e fúngicas ao longo do tempo (aumento no escore de diversidade microbiana: enzima 38%, clorexidine 11%, controle5%) e a abundância relativa de patógenos reduziu significativamente (enzima, P = 0,028; CHX, P = 0,048). Observou-se uma correlação clara (r

Catalases play a key role in the defense against oxidative stress in bacteria by catalyzing the decomposition of H2O2. In addition, catalases are also involved in multiple cellular processes, such as cell development and differentiation, as well as metabolite production. However, little is known about the abundance, diversity, and distribution of catalases in bacteria. In this study, we systematically surveyed and classified the homologs of three catalase families from 2,634 bacterial genomes. It was found that both of the typical catalase and Mn-catalase families could be divided into distinct groups, while the catalase-peroxidase homologs formed a tight family. The typical catalases are rich in all the analyzed bacterial phyla except Chlorobi, in which the catalase-peroxidases are dominant. Catalase-peroxidases are rich in many phyla, but lacking in Deinococcus-Thermus, Spirochetes, and Firmicutes. Mn-catalases are found mainly in Firmicutes and Deinococcus-Thermus, but are rare in many other phyla. Given the fact that catalases were reported to be involved in secondary metabolite biosynthesis in several Streptomyces strains, the distribution of catalases in the genus Streptomyces was given more attention herein. On average, there are 2.99 typical catalases and 0.99 catalase-peroxidases in each Streptomyces genome, while no Mn-catalases were identified. To understand detailed properties of catalases in Streptomyces, we characterized all the five typical catalases from S. rimosus ATCC 10970, the oxytetracycline-producing strain. The five catalases showed typical catalase activity, but possessed different catalytic properties. Our findings contribute to the more detailed classification of catalases and facilitate further studies about their physiological roles in secondary metabolite biosynthesis and other cellular processes, which might facilitate the yield improvement of valuable secondary metabolites in engineered bacteria.

The multi-domain bacterial S1 protein is the largest and most functionally important ribosomal protein of the 30S subunit, which interacts with both mRNA and proteins. The family of ribosomal S1 proteins differs in the classical sense from a protein with tandem repeats and has a "bead-on-string" organization, where each repeat is folded into a globular domain. Based on our recent data, the study of evolutionary relationships for the bacterial phyla will provide evidence for one of the proposed theories of the evolutionary development of proteins with structural repeats: from multiple repeats of assembles to single repeats, or vice versa. In this comparative analysis of 1333 S1 sequences that were identified in 24 different phyla, we demonstrate how such phyla can form independently/dependently during evolution. To the best of our knowledge, this work is the first study of the evolutionary history of bacterial ribosomal S1 proteins. The collected and structured data can be useful to computer biologists as a resource for determining percent identity, amino acid composition and logo motifs, as well as dN/dS ratio in bacterial S1 protein. The obtained research data indicate that the evolutionary development of bacterial ribosomal S1 proteins evolved from multiple assemblies to single repeat. The presented data are integrated into the server, which can be accessed at http://oka.protres.ru:4200.

Short-term composting of raw materials for preparing oyster mushroom cultivation media is widely used in China, and its microbial mechanism needs to be further studied. 11-days' peach sawdust-based composting was performed to evaluate material conversion and microbial succession using physicochemical analysis and 16S rRNA and ITS sequencing. Composting bacteria demonstrated much higher abundance than fungi. Firmicutes, Actinobacteriota, and Proteobacteria were the dominant bacterial phyla, while most of fungal species belonged to Ascomycota. Moisture was the key factor at the beginning, while total nitrogen, temperature, and lignin became main influencing factors for composting maturity. Actinobacteriota, Firmicutes, and Proteobacteria of bacterial phyla, Eurotiomycetes and Sordariomycetes of fungal classes involved in lignocellulosic degradation. Bacterial function prediction analysis showed that carbohydrate metabolism and amino acid metabolism were the main metabolic pathways. These results confer a better understanding of material and microbial succession during short-term composting and also provide valuable utilization in mushroom industry.

Background Dendrobium is a precious herbal that belongs to Orchidaceae and is widely used as health care traditional Chinese medicine in Asia. Although orchids are mycorrhizal plants, most research still focuses on endophytes, and there is still large amount unknown about rhizosphere microorganisms. To investigate the rhizosphere microbial community of different Dendrobium species during the maturity stage, we used high-throughput sequencing to analyze microbial community in rhizosphere soil during the maturity stage of three kinds of Dendrobium species. Results In our study, a total of 240,320 sequences and 11,179 OTUs were obtained from these three Dendrobium species. According to the analysis of OTU annotation results, different Dendrobium rhizosphere soil bacteria include 2 kingdoms, 63 phyla, 72 classes, 159 orders, 309 families, 850 genera and 663 species. Among all sequences, the dominant bacterial phyla (relative abundance > 1%) were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, Chloroflexi, and Gemmatimonadetes. And through WGCNA analysis, we found the hub flora was also belong to Acidobacteria, Actinobacteria and Proteobacteria. Conclusions We found that the rhizosphere bacterial communities of the three kinds of Dendrobium have significant differences, and that the main species of rhizosphere microorganisms of Dendrobium are concentrated in the Proteobacteria, Actinobacteria, and Bacteroidetes. Moreover, the smaller the bacterial level, the greater the difference among Dendrobium species. These results fill knowledge gaps in the rhizosphere microbial community of Dendrobium and provide a theoretical basis for the subsequent mining of microbial functions and the study of biological fertilizers.

Purpose Childhood malnutrition is a multifactorial disease, responsible for nearly half of all deaths in children under five. Lately, the probable association of a dysbiotic gut to malnutrition is also being eagerly investigated. The current study is an attempt to investigate this purported association through assessing the abundance of major gut bacterial phyla (Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria), probionts (Bifidobacteria and Lactobacillus), butyrogens (Faecalibacterium and Roseburia) and pathogens (Escherichia and Klebsiella). Methods The study was conducted in the suburbs of Chandigarh, India in the year 2017. The children enrolled in the study were part of Anganwadis (Rural Child Care Centres) set up under Integrated Child Development Scheme (ICDS) of Government of India where community-based management approach is being widely used for treatment of malnutrition. We used qPCR based absolute quantification as well as the 16S rRNA amplicon sequencing approach for our study. The study population included 30 children in the age group of 2–5 years who were categorized into three groups Healthy, Moderate Acute Malnutrition (MAM) and Severe Acute Malnutrition (SAM), with 10 children in each group. The selection of participants was made based on Z scores. Further, statistical tools like the One-way ANOVA, PCA and PLSDA were employed to analyze and compare the gut bacterial profile. Results Our investigation through the qPCR (Absolute quantification) approach revealed a significantly higher abundance of Actinobacteria in healthy, in comparison to children suffering from Severe Acute Malnutrition (SAM). Consequently, the same trend was also reflected with respect to Bifidobacterium, a prominent member of the Actinobacteria phylum. Conversely, a significant higher abundance of Lactobacillus with the diminishing nutritional status was recorded. Escherichia showed a significant higher abundance in healthy subjects compared to the malnourished; however, no such difference in abundance of Klebsiella was observed. The other target phyla [Bacteroidetes, Firmicutes and Proteobacteria] and genera (Faecalibacterium and Roseburia) showed differences in abundance; however, these were non-significant. Similarly, the bacterial taxonomy analysis of 16S rRNA gene amplicon sequencing data revealed the higher abundance of phylum Actinobacteria and its member Bifidobacterium with lower prevalence of Lactobacillus in healthy children. Conclusion The pattern of gut microbiota profile in malnourished subjects suggests a dysbiotic gut depleted in Bifidobacteria, a core member of the consortia of beneficial anaerobes of the healthy child gut. Supplementary Information The online version contains supplementary material available at 10.1007/s00394-021-02571-7.

Insects represent the most successful taxon of eukaryotic life, being able to colonize almost all environments. Microbial symbiomes associated with insects, impact important physiologies, and influence nutritional and immune system status, and ultimately, fitness. A variety of bacterial phyla are commonly present in insect guts, including Gammaproteobacteria, Alphaproteobacteria, Betaproteobacteria, Bacteroidetes, Firmicutes, Clostridia, Spirochetes, Verrucomicrobia, Actinobacteria, and others. Among them, the genus Enterobacter has been recognized as a dominant inhabitant of the gut for several important insect species, indicating an essential functional role for this taxon. Here, we review the known Enterobacter functional diversity among insects with respect to insect development, host exploitation, reproduction, and interactions with other organisms, in an attempt to provide an overview of the traits that have resulted in their evolutionary success. Many strains of Enterobacter species are not simply insect commensals but confer beneficial traits to their hosts that primarily fall into two categories: provision and degradation of nutrients and protection from pathogens.

Xiaoqu, one of three traditional jiuqu in China, is a saccharifying and fermenting agent used in Xiaoqu jiu brewing, with different ingredient compositions and preparation techniques used in various regions. The yield and quality of Xiaoqu jiu are significantly affected by the metabolites and microbiota of Xiaoqu; however, the associated relationship remains poorly understood. This study aimed to analyze this relationship in three typical traditional Xiaoqu from the Guizhou province in China. The non-volatile metabolites of Xiaoqu were detected using gas chromatography time-of-flight mass spectrometry, whereas the classification and metabolic potential of the microbiota were investigated using metagenomic sequencing. Results show that Firmicutes, Proteobacteria, and Actinobacteria represent the dominant bacterial phyla, with Lactobacillus, Bacillus, Acinetobacter, Leuconostoc, and Weissella found to be the dominant bacterial genera. Meanwhile, Ascomycota, Mucoromycota, and Basidiomycota are the dominant fungal phyla with Aspergillus, Saccharomyces, Pichia, Rhizopus, and Phycomyces being the predominant fungal genera. Functional annotation of the microbiota revealed a major association with metabolism of carbohydrates, cofactors, and vitamins, as well as amino acids. A total of 39 significantly different metabolites (SDMs) were identified that are involved in 47 metabolic pathways, primarily that of starch and sucrose; glycine, serine, and threonine; glyoxylate and dicarboxylate; pyruvate; as well as biosynthesis of pantothenate and CoA. Further, based on Spearman's correlation analysis, Aspergillus, Saccharomyces, Lactobacillus, Acetobacter, Weissella, Pantoea, Desmospora, and Bacillus are closely correlated with production of physicochemical indexes and SDMs. Moreover, the metabolic network generated for the breakdown of substrates and formation of SDMs in Xiaoqu was found to primarily center on the metabolism of carbohydrates and the tricarboxylic acid cycle. These results provide insights into the functional microorganisms and metabolic patterns present in traditional Guizhou Xiaoqu and might guide researchers in the production of stable and efficient Xiaoqu in the future.

In Leptinotarsa decemlineata, a final-instar wandering larva typically undergoes an ontogenetic niche shift (ONS), from potato plant during the foraging stage to its pupation site below ground. Using high-throughput sequencing of the bacterial 16S ribosomal RNA gene, we determined the hypothesis that the L. decemlineata pupae harbor stage-specific bacteria to meet the physiological requirements for underground habitat. We identified 34 bacterial phyla, comprising 73 classes, 208 orders, 375 families, and 766 genera in the collected specimens. Microbes across phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were enriched in the pupae, while those in the phylum Proteobacteria, Tenericutes, Firmicutes, and Bacteroidetes dominated in the larvae and adults. A total of 18 genera, including Blastococcus, Corynebacterium_1, Gordonia, Microbacterium, Nocardia, Nocardioides, Rhodococcus, Solirubrobacter, Tsukamurella, Enterococcus, Acinetobacter, Escherichia_Shigella, Lysobacter, Pseudomonas, and Stenotrophomonas, were specifically distributed in pupae. Moreover, soil sterilizing removed a major portion of bacteria in pupae. Specifically, both Enterococcus and Pseudomonas were eliminated in the soil sterilizing and antibiotic-fed beetle groups. Furthermore, the pupation rate and fresh pupal weight were similar, whereas the emergence rate and adult weight were decreased in the antibiotic-fed beetles, compared with controls. The results demonstrate that a switch of bacterial communities occurs in the pupae; the pupal-specific bacteria genera are mainly originated from soil; this bacterial biodiversity improves pupa performance in soil. Our results provide new insight into the evolutionary fitness of L. decemlineata to different environmental niches.

Epinephelus coioides, or grouper, is a high economic value fish species that plays an important role in the aquaculture industry in Asia. However, both viral and bacterial diseases have threatened grouper for many years, especially nervous necrosis virus, grouper iridovirus and Vibrio harveyi, which have caused a bottleneck in the grouper industry. Currently, intestinal microbiota can provide novel insights into the pathogenesis-related factors involved in pathogen infection. Hence, we investigated the comparison of intestinal microbiota communities in control group and pathogen-infected grouper through high-throughput sequencing of the 16S rRNA gene. Our results showed that microbial diversity was decreased, whereas microbial richness was increased during pathogen infection. The individuals in each group were distributed distinctly on the PLSDA diagram, especially the GIV group. Proteobacteria and Firmicutes were the most abundant bacterial phyla in all groups. Interestingly, beneficial genera, Faecalibacterium and Bifidobacterium, predominated in the intestines of the control group. In contrast, the intestines of pathogen-infected grouper had higher levels of harmful genera such as Sphingomonas, Atopostipes, Staphylococcus and Acinetobacter. Additionally, we investigated the expression levels of innate and adaptive immune-related genes after viral and bacterial infection. The results revealed that immunoglobulin T and proinflammatory cytokine levels in the intestine increased after pathogen infection. Through these unique bacterial compositions in diseased and uninfected fish, we could establish a novel therapeutic approach and bacterial marker for preventing and controlling these diseases.