Phyla Of Bacteria Research Articles

Gut Microbiota Profile in Adults Undergoing Bariatric Surgery: A Systematic Review.

Gut microbiota (GM) after bariatric surgery (BS) has been considered as a factor associated with metabolic improvements and weight loss. In this systematic review, we evaluate changes in the GM, characterized by 16S rRNA and metagenomics techniques, in obese adults who received BS. The PubMed, Scopus, Web of Science, and LILACS databases were searched. Two independent reviewers analyzed articles published in the last ten years, using Rayyan QCRI. The initial search resulted in 1275 documents, and 18 clinical trials were included after the exclusion criteria were applied. The predominance of intestinal bacteria phyla varied among studies; however, most of them reported a greater amount of Bacteroidetes (B), Proteobacteria (P), and diversity (D) after BS. Firmicutes (F), B, and the (F/B) ratio was inconsistent, increasing or decreasing after Roux-en-Y gastric bypass (RYGB) and sleeve gastrectomy (SG) were conducted, compared to before surgery. There was a reduction in the relative proportion of F. Moreover, a higher proportion of Actinobacteria (A) was observed after RYGB was conducted. However, the same was not identified when SG procedures were applied. Genera abundance and bacteria predominance varied according to the surgical procedure, with limited data regarding the impact on phyla. The present study was approved by PROSPERO, under registration number CRD42020209509.

Maize rhizosphere modulates the microbiome diversity and community structure to enhance plant health

Metagenomic has been explored in investigating microbiome diversity. However, there is limited available information on its application towards securing plant health. Hence, this study adopts the metagenomic approach to unravel the microbiome diversity associated with healthy (LI and MA) and Northern corn leaf blight (NCLB) infected (LID and MAD) maize rhizosphere in the maize growing field at Lichtenburg and Mafikeng, North-West province of South Africa. The extraction of whole DNA from the respective healthy and diseased rhizosphere soils was conducted and sequenced using shotgun metagenomics. A total of 12 bacteria, 4 archaea and 2 fungal phyla were found as predominant across the fields with the use of the SEED subsystem database. The most predominant bacteria phyla included Proteobacteria, Dienococcus-Thermus, Gemmatimonadetes, Chlorobi, Cyanobacteria, Planctomycetes, Verrucomicrobia, Acidobacteria, Firmicutes, Chloroflexi and Bacteroidetes. Archaea consisted of Euryarchaeota, Thaumarchaeota, Crenarchaeota and Korachaeota, while Ascomycota and Basidiomycota were the dominant fungal phyla. Microbial abundance and diversity were higher in the rhizosphere of healthy maize (LI and MA) rhizosphere as compared to the NCLB diseased (LID and MAD), in the order LI > MA > LID > MAD. At phylum and genus level, alpha diversity index showed no significant (p > 0.05) difference in the abundance of the microbial community of healthy and NCLB infected maize rhizosphere, while beta analysis produced a significant (p = 0.01) difference in the microbial diversity in the soil. Taken together, the study revealed that the abundance of microbial diversity in the maize rhizosphere influences the efficacy of the rhizosphere microbiome to modulate microbial functions towards managing and sustaining plant health.

Microbiota structure and diversity in Aedes albopictus at different developmental stages

To investigate the diversity and composition of microflora in laboratory-reared Aedes albopictus at different developmental stages and larval habitat waters. The larval habitat waters and different developmental stages of laboratory-reared A. albopictus were collected, and the V3 and V4 regions of the bacterial 16S rRNA gene were sequenced using Illumina Miseq next-generation sequencing. The abundance and diversity of the microflora were examined using alpha diversity index in A. albopictus at different developmental stages, and the difference in the microflora compositions was compared in A. albopictus at different developmental stages using principal component analysis (PCA). In addition, the species composition and relative abundance of microflora in A. albopictus at different developmental stages were described using histograms and Venn diagrams. A total of 16 phyla, 30 classes, 72 orders, 129 families and 224 genera of bacteria were detected in larval habitat waters and different developmental stages of A. albopictus. The highest bacterial diversity was seen in larval A. albopictus, with Chao index of 125.20 ± 30.48 and Shannon diversity index of 2.04 ± 0.39, which were comparable to those (Chao index of 118.52 ± 15.07 and Shannon diversity index of 2.15 ± 0.30) in larval habitat waters (t = 0.35 and -0.41, both P values > 0.05). The bacterial abundance and evenness were significantly greater in female adults than in male adults (Chao index: 42.50 ± 3.54 vs. 18.50 ± 2.13, t = 8.23, P < 0.05; Shannon diversity index: 1.25 ± 1.67 vs. 0.50 ± 0.05, t = 6.00, P < 0.05). Proteobacteria, Bacteroidota, Actinobacteriota and Finnicutes were four common phyla of bacteria at each developmental stage of A. albopictus, with Proteobacteria dominated at the pupal stage (90.36%), Bacteroidota dominated at the adult stage (46.01% in female adults and 86.11% in male adults), and Actinobacteriota dominated at the larval stage (32.10%). Elizabethkingia and Rahnella 1 were common dominant genera of bacteria at each developmental stage of A. albopictus, with Rahnellal as the major component at the pupal stage (87.56%), Elizabethkingia as the main component at the adult stage (46.01% in female adults and 86.11% in male adults, respectively), and Microbacteria as the dominant bacterial genus at the larval stage (12.11%). In addition, Delftia, Elizabethkingia, Romboutsia, Serratia, Rahnella 1, Enterococcus and Microbacterium were common genera of bacteria at each developmental stage of A. albopictus, with Edaphobaculum dominated at the larval stage (17.54%) and Sphingobacterium dominated in larval habitat waters (13.93%). There are differences in the composition of symbiotic bacteria at different developmental stages of A. albopictus; however, similar microflora diversity is maintained at the phylum level. The microflora diversity is comparable in larvae and larval habitat waters of A. albopictus.

Developmental stage variation in the gut microbiome of South China tigers.

South China tigers (Panthera tigris amoyensis, SC) are the most threatened tiger subspecies in the world. All the living SCs are captive in zoos or reserves and depend on artificial feeding. The composition of the gut microbiome plays an important role in sustaining the health of the host. A comprehensive understanding of the composition and development of the microbial community of SC is helpful to improve the feeding of captive SC. In this study, we collected 47 fecal samples, 37 of which were from SC of three developmental stages, 5 from adult Amur tigers (Am), and 5 from adult Bengal tigers (Bg), which were all housed in the same zoo. We investigated the diversity, richness, and composition of the bacterial microbiomes and we found that the gut microbiome of SC is strongly affected by host aging. The composition of the gut microbiome of juvenile SC experienced dramatic changes from 5 months old to 1 year old, and it showed much less difference when compared to the samples of 1 year old and the subadult. No significant differences were observed between the samples of subadult and the adult groups. The predominant phylum of 5-month-old SC is Fusobacteriota (33.99%) when the juvenile tigers were older than 5 months, and Firmicutes, but not Fusobacteriota, became the predominant phylum of bacteria in their gut. The gut microbiome of SC, Am, and Bg is possibly affected by their genetic variation; however, the core microbiome of these three subspecies is the same. Our data suggest that the gut microbiome of SC undergoes a developmental progression: a developmental phase (cub), a transitional phase (subadult), and a stable phase (adult). These results expand our understanding of the role of age in the development of the gut microbiome of SC.

Diversity and Taxonomy of Soil Bacterial Communities in Urban and Rural Mangrove Forests of the Panama Bay.

Mangrove ecosystems are threatened worldwide by a wide range of factors including climate change, coastal development, and pollution. The effects of these factors on soil bacterial communities of Neotropical mangroves and their temporal dynamics is largely undocumented. Here we compared the diversity and taxonomic composition of bacterial communities in the soil of two mangrove forest sites of the Panama Bay: Juan Diaz (JD), an urban mangrove forest in Panama City surrounded by urban development, with occurrence of five mangrove species, and polluted with solid waste and sewage; and Bayano (B), a rural mangrove forest without urban development, without solid waste pollution, and with the presence of two mangrove species. Massive amplicon sequencing of the V4 region of the 16S rRNA gene and community analyses were implemented. In total, 20,691 bacterial amplicon sequence variants were identified, and the bacterial community was more diverse in the rural mangrove forest based on Faith's phylogenetic diversity index. The three dominant phyla of bacteria found and shared between the two sites were Proteobacteria, Desulfobacterota, and Chloroflexi. The ammonia oxidizing archaea class Nitrosphaeria was found among the top 10 most abundant. Dominant genera of bacteria that occurred in the two mangrove sites were: BD2-11_terrestrial_group (Gemmatimonadota), EPR3968-O8a-Bc78 (Gammaproteobacteria), Salinimicrobium (Bacteroidetes), Sulfurovum (Campylobacteria), and Woeseia (Gammaproteobacteria) of which the first three and Methyloceanibacter had increased in relative abundance in the transition from rainy to dry to rainy season in the urban mangrove forest. Altogether, our study suggests that factors such as urban development, vegetation composition, pollution, and seasonal changes may cause shifts in bacterial diversity and relative abundance of specific taxa in mangrove soils. In particular, taxa with roles in biogeochemical cycles of carbon, nitrogen, sulfur, and phosphorus, and on rhizosphere taxa, could be important for mangrove plant resilience to environmental stress.

Effects of Hericium erinaceus Hedgehog mushroom on the endophytic microbial community of the host plant.

Hedgehog mushroom is a Hericium erinaceus associated with fagaceae and pinaceae trees in the northern hemisphere. It is still unknown whether this symbiotic relationship will affect the endophytic microbial community of the host plants. In this study, the endophytic microbial communities of different Quercus aliena tissues (root, stem, and leaf) with or without H. erinaceus partner were analyzed by bar-coded pyrosequencing. About 29,000 clean reads were obtained per sample representing 28 phyla of bacteria and 6 phyla of fungi. A total of 26,838 operational taxonomic units (OTUs) of bacteria and 4323 OTUs of fungi were observed at a 97% similarity level. Three bacterial phyla, Proteobacteria, Cyanobacteria and Bacteroidetes, and fungal phylum Ascomycota were dominant in all tissues. The relative abundance of these dominant communities showed significantly differences between Q. aliena tissues with or without H. erinaceus. Bacterial genus Pseudomonas and fungal genus Cryptosporiopsis were species-rich in Q. aliena root infected by H. erinaceus hyphae. This study demonstrated that the endophytic microbial community structure and dominant species varied in Q. aliena mycorrhized with H. erinaceus.

Study on microbes and antibiotic resistance genes in karst primitive mountain marshes – A case study of Niangniang Mountain in Guizhou, China

Previous research on antibiotic resistance genes and microorganisms centered on those in urban sewage treatment plants, breeding farms, hospitals and others with serious antibiotic pollution. However, at present, there are evident proofs that antibiotic resistance genes (ARGs) indeed exist in a primitive environment hardly without any human’s footprints. Accordingly, an original karst mountain swamp ecosystem in Niangniang Mountain, Guizhou, China, including herbaceous swamp, shrub swamp, sphagnum bog and forest swamp, was selected to analyze the physical and chemical parameters of sediments. Moreover, microbial compositions, functions, as well as their connections with ARGs were assayed and analyzed using metagenomic technology. The results showed that there was no significant difference in the dominant microorganisms and ARGs in the four marshes, in which the dominant bacteria phyla were Proteobacteria (37.82 %), Acidobacteriota (22.17 %) and Actinobacteriota (20.64 %); the dominant archaea Euryarchaeota. (1.00 %); and the dominant eukaryotes Ascomycota (0.07 %), with metabolism as their major functions. Based on the ARDB database, the number of ARGs annotated reached 209 including 30 subtypes, and the dominant ARGs were all Bacitracin resistance genes (bacA, 84.77 %). In terms of the diversity of microorganisms and ARGs, the herbaceous swamp ranked the top, and the shrub swamp were at the bottom. Correlation analysis between microorganisms and resistance genes showed that, apart from aac2ic, macB, smeE, tetQ, and tetL, other ARGs were positively correlated with microorganisms. Among them, baca coexisted with microorganisms. Pearson correlation analysis results showed that contrary to ARGs, microorganisms were more affected by environmental factors.

Improving the removal efficiency of nitrogen and organics in vertical-flow constructed wetlands: the correlation of substrate, aeration and microbial activity.

Four vertical-flow CWs (VFCWs) with different substrates and aeration conditions were studied on nutrient-removal capacity from synthetic wastewater. Zeolite substrate VFCWs (none-aerated: VFCW-1, aerated: VFCW-3) paralleled with ceramsite (none-aerated:VFCW-2, aerated: VFCW-4) were used to study the removal efficiencies of N and organics, the bacterial community, and the related functional genes. The results indicated that the pollutant removal efficiency was significantly enhanced by intermittent aeration. VFCW-4 (ceramsite with aeration) demonstrated a significant potential to remove NH4+-N (89%), NO3--N (78%), TN (71%), and COD (65%). VFCW-3 and VFCW-4 had high abundances of Amx, amoA, and nirK genes, which was related to NH4+-N and NO2--N removal. The microbial diversity and structure varied with aeration and substrate conditions. Proteobacteria, Actinobacteria, Candidatus, and Acidobacteria were the main bacteria phyla, with the average proportion of 38%, 21%, 19%, and 7% in the VFCWs. Intermittent aeration increased the abundance of Acidobacteria, which was conducive to the removal of organic matters. Overall, ceramsite substrate combined with intermittent aeration has a great potential in removing pollutants in VFCWs.

Oral microbiota in oral cancer patients and healthy individuals: A scoping review

Background: Oral microbiota has been suggested to have a role in the etiopathogenesis of oral cancer; however, the oral microbiota diversity in patients with oral cancer compared to healthy individuals remains unclear. Purpose: This scoping review aimed to provide an overview of the current evidence regarding the oral microbiota composition colonized in oral cancer patients and its comparison with healthy individuals. Reviews: This study was conducted according to the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines. Eligible studies were searched in PubMed, Scopus, Web of Science, and ScienceDirect databases from January 2015 to March 2022. A total of 20 relevant studies were included according to the inclusion and exclusion criteria, including 14 cross-sectional studies and 6 cohort studies. All studies have identified various oral bacteria, but only one study has detected viruses and parasites diversity. A variety of oral microbiota found were 6 phyla of bacteria, 6 phyla of viruses, 7 phyla of fungi, and 7 phyla of parasitic. Seventeen studies proved that oral microbiota compositions were statistically significant differences compared to healthy controls, but not in 3 studies. Conclusion: The majority of studies showed various oral bacteria in oral cancer patients which were statistically significant difference compared to healthy controls. This study indicates the need for more research to evaluate viruses and parasites composition and diversity in oral cancer patients. Moreover, future research should focus to clarify whether the changes of oral microbial composition as a community may play a critical role in the etiopathogenesis of oral cancer.

Changes in the population and functional profile of bacteria and fungi in the rhizosphere of Suaeda salsa is driven by invasion of Spartina alterniflora

Changes in rhizosphere microbial populations and their functions in response to Spartina alterniflora root invasion could potentially reveal part of the mechanism of Suaeda salsa degradation. In this study, rhizosphere soils were collected from regions where S. alterniflora (SA) and S. salsa (SS) grew independently as well as rhizosphere soil from mixed growth regions (namely MSA and MSS) before applying high-throughput sequencing technology to study the characteristics of microbial communities. The results showed that the physicochemical properties of the rhizosphere soils were different between the groups of samples. However, based on the multi-factor PERMANOVA analysis, only EC and NO3−-N were found to significantly influence the microbial communities’ composition. Furthermore, α diversity indices and β diversity analyses revealed that the diversity and structure of rhizosphere microbial community changed in varying degrees after invasion. Compared with SS, the most abundant bacteria phylum namely Tenericutes, Firmicutes, Proteobacteria and Actinobacteria in MSS were identified as major species that increased significantly in abundance in response to S. alterniflora root invasion, while the composition of fungal community did not change. Furthermore, PICRUSt analysis revealed that the higher abundance of signal transduction, membrane transport, cell motility and certain disease-related functional pathways of MSA and MSS could be conducive to the colonization and survival of bacterial pathogens. Additionally, the analysis of the FUNGuild database confirmed that a higher proportion of pathotroph and pathogen. This could very likely cause S. salsa to be more susceptible to soil pathogenic fungi in mixed growth region. In contrast, the increase of the saprotroph-symbiotroph could be beneficial for the colonization and expansion of S. alterniflora. This study provides a new perspective for elucidating the driving mechanism by microorganisms behind S. salsa’s degradation following S. alterniflora’s invasion.

Cholesterol supplementation improved growth performance, cholesterol metabolism, and intestinal health of Pacific white shrimp (Litopenaeus vannamei) fed a low fishmeal diet

An 8-weeks feeding trial was conducted to evaluate the effects of dietary cholesterol supplementation on growth performance, hemolymph biochemical parameters, cholesterol metabolism, intestinal health, and disease resistance of Pacific white shrimp (Litopenaeus vannamei) fed a low fishmeal diet. Four experimental diets including HFM (25% fishmeal), LFM (15% fishmeal+10% soy protein concentrate), LC1 (LFM+0.6 g kg−1 cholesterol), and LC2 (LFM+1.2 g kg−1 cholesterol) were formulated, each diet was fed to quadruplicate tanks with 40 shrimp (0.33 ± 0.03 g) per tank for 56 days. The results shown that cholesterol supplementation in the diet did not affect the growth performance of Litopenaeus vannamei (P > 0.05), but the crude lipid content significantly reduced in the LC2 group than that in HFM group (P < 0.05). In the hemolymph biochemical indices, the content of total cholesterol in LFM and LC1 groups were significantly lower than that in HFM group; the HDL-C content was significantly lower in the shrimp fed low fishmeal based-diets (LFM, LC1, and LC2) than those fed in HFM diet; the TG content of two cholesterol supplemented groups were significantly lower than that of HFM group; the MDA content was significantly higher in LFM group than that in HFM group (P < 0.05). In hepatopancreas lipid metabolism, the shrimp fed LFM diet has higher expression in srebp, fas, and acc than those fed the HFM diet, and two cholesterol groups significant decreased the acc relative expression compare with LFM group; compare with HFM group, the LFM group showed significantly up-regulated hmg-CoA, npc1 relative expression, and LC1 group significantly up-regulated scp relative expression, then LC2 group significantly up-regulated scp, npc2 relative expression of hepatopancreas in cholesterol metabolism; LFM, LC1 group significantly up-regulated beclin1, atg12 relative expression and LC2 group up-regulated beclin1 relative expression than those in HFM group of hepatopancreas in cell autophagy (P < 0.05). LC1 group up-regulated imd, relish, toll, myd88, pelle, tube, and dorsal relative expression and LC2 group up-regulated ikkβ, myd88, tube, and dorsal relative expression in intestinal immunity than those in HFM group (P < 0.05). Cholesterol supplementation increased the height of the intestinal folds of shrimp fed the low fishmeal based-diets (P < 0.05), as well as improved the integrity of the mitochondria and the endoplasmic reticulum. Dietary cholesterol supplementation decreased the abundance of harmful bacteria phylum (Chlamydiae) and increased the abundance of beneficial bacteria genus (Pseudoalteromona, Rhodopirellula, and Ruegeria) compared with LFM group (P < 0.05). Shrimp fed the LC1 diet showed higher resistance to V. parahaemolyticus challenge than those fed the LFM diet (P < 0.05). In conclusion, cholesterol supplementation in a low fishmeal diet significantly enhanced the lipolytic capacity of shrimp, promoted the cellular autophagy, improved the intestinal health, and enhanced disease resistance of Litopenaeus vannamei.

The gut microbiota regulates acute foreign body reaction and tissue repair after biomaterial implantation

We hypothesized that the host microbiome may influence foreign body responses following biomaterial implantation. To test this, we implanted a variety of clinically relevant biomaterials into germ-free or antibiotic-treated mice. Surprisingly, these mice displayed less fibrous tissue deposition, reduced host cell recruitment to the implant site, and differential expression of angiogenic and inflammatory markers. These observations were reversed upon fecal microbiome reconstitution, confirming a causal role of the host microbiome. In a clinically relevant disease model, microbiome-depleted mice cleared hyaluronic acid and bone marrow mononuclear cells from ischemic hind limb tissues more slowly, resulting in an improved therapeutic response. Findings were confirmed in pigs which showed reduced fibrotic responses to a variety of implanted materials. Lastly, we profiled changes in the host microbiome following material implantation, implicating several key bacteria phyla.

Assembling microbial communities: a genomic analysis of a natural experiment in neotropical bamboo internodes.

Microbes participate in ecological communities, much like multicellular organisms. However, microbial communities lack the centuries of observation and theory describing and predicting ecological processes available for multicellular organisms. Here, we examine early bacterial community assembly in the water-filled internodes of Amazonian bamboos from the genus Guadua. Bamboo stands form distinct habitat patches within the lowland Amazonian rainforest and provide habitat for a suite of vertebrate and invertebrate species. Guadua bamboos develop sealed, water-filled internodes as they grow. Internodes are presumed sterile or near sterile while closed, but most are eventually opened to the environment by animals, after which they are colonized by microbes. We find that microbial community diversity increases sharply over the first few days of environmental exposure, and taxonomic identity of the microbes changes through this time period as is predicted for early community assembly in macroscopic communities. Microbial community taxonomic turnover is consistent at the bacteria phylum level, but at the level of Operational Taxonomic Units (OTUs), internode communities become increasingly differentiated through time. We argue that these tropical bamboos form an ideal study system for microbial community ecology due to their near-sterile condition prior to opening, relatively consistent environment after opening, and functionally limitless possibilities for replicates. Given the possible importance of opened internode habitats as locations of transmission for both pathogenic and beneficial microbes among animals, understanding the microbial dynamics of the internode habitat is a key conservation concern for the insect and amphibian species that use this microhabitat.

Response of Soil Microbial Community Composition and Diversity at Different Gradients of Grassland Degradation in Central Mongolia

Vegetation and soil microorganisms are important components of terrestrial ecosystems and play a crucial role in ecosystem functioning. However, little is known about the synergistic changes in soil microbial community with aboveground plants in grassland degradation and the role of the microbial community in the process of vegetation restoration succession. In this study, we investigated the characteristics of soil microbial communities and diversities in the different levels of grassland degradation using Illumina MiSeq high-throughput sequencing. The dominant bacteria phyla were: Actinobacteriota, 31.61–48.90%; Acidobacteriota, 7.19–21.73%; Chloroflexi, 9.08–19.09%; and Proteobacteria, 11.14–18.03%. While the dominant fungi phyla were: Ascomycota, 46.36–81.58%; Basidiomycota, 5.63–33.18%; and Mortierellomycota, 1.52–37.69%. Through RDA/CCA, the effects of environmental factors on the differences in the soil microbial community between different sites were interpreted. Results showed that the pH was the most critical factor affecting soil microbial communities in seriously degraded grassland; nevertheless, soil microbial communities in non-degraded grassland and less degraded grasslands were mainly affected by the soil moisture content and soil enzyme activities (sucrase activity, alkaline phosphatase activity and catalase activity). We systematically demonstrated the soil microbial communities of different grassland degradation gradients in Mongolia, which provided valuable information for grassland degradation reduction and vegetation restoration succession.

Spatial Distribution of Quinolone Antibiotics and Its Correlation Relationship with Microbial Community in Soil of Shijiazhuang City

Microbial communities are an important component of soil ecosystems. Long-term low content antibiotic pollution will affect the structure and function of microbial communities in soil. Therefore, Shijiazhuang City was selected as the study area, in which twelve sample points were set up in September 2020. These sample sites were divided into four areas (S1, S2, S3, and S4) according to spatial orientation. Ultra-high performance liquid chromatography-mass spectrometry (HPLC-MS/MS) was applied to determine the content of typical antibiotic-quinolones (QNs) in the soil. 16S rRNA high-throughput sequencing technology was used to study the microbial community structure and diversity in the soil. The results showed that:① the total detected contents of QNs in the four areas were S3 (313.5 μg·kg-1)>S4 (65.54 μg·kg-1)>S1 (46.19 μg·kg-1)>S2 (12.63 μg·kg-1). The content of norfloxacin (NOR) was the highest (91.99 μg·kg-1), whereas the content of oxolinic acid (OXO) was the lowest (0.4486 μg·kg-1). ② For grain size, the proportion of powder (2-50 μm) was the highest (66.7%-93.2%), whereas the proportion of clay (less than 2 μm) was the lowest (2.50%-9.10%). For physical and chemical parameters, total phosphorus (TP) and ammonia nitrogen (NH4+-N) showed non-significant spatial differences, whereas nitrate nitrogen (NO3--N), nitrite nitrogen (NO2--N), and grain size showed significant spatial differences. ③ For microbial community composition, there were six dominant bacteria phyla and five dominant bacteria genera, among which Actinobacteriota (18.3%-34.6%) and Proteobacteria (13.6%-34.1%) were the dominant bacteria phyla, and Arthrobacter (3.24%-8.61%) and Nitrososphaeraceae (2.93%-9.46%) were the dominant bacteria genera. The diversity results showed the highest value in the S2 area (6.48) and the lowest value in the S3 area (5.89). ④ QNs and soil physical and chemical parameters significantly changed the structural composition of microbial communities, and OXO, NO3--N, and soil particle size affected the diversity of microbial communities. FLU, NH4+-N, NO2--N, and soil particle size affected the function of the microbial community. Therefore, it is necessary to further strengthen the risk control of antibiotics in the soil of Shijiazhuang City.

First determination of DNA virus and some additional bacteria from Melophagus ovinus (sheep ked) in Tibet, China.

Melophagus ovinus (sheep ked) is one of the common ectoparasites in sheep. In addition to causing direct damage to the host through biting and sucking blood, sheep ked is a potential vector of helminths, protozoa, bacteria, and viruses. Sheep M. ovinus samples from three regions in Tibet were selected for DNA extraction. The 16S rDNA V3-V4 hypervariable region was amplified, after genomic DNA fragmentation, Illumina Hiseq libraries were constructed. The 16S rRNA sequencing and viral metagenomics sequencing were separately conducted on the Illumina Novaseq 6000 platform and molecular biology software and platforms were employed to analyze the sequencing data. Illumina PE250 sequencing results demonstrated that the dominant bacteria phylum in M. ovinus from Tibet, China was Proteobacteria, where 29 bacteria genera were annotated. The dominant bacterial genera were Bartonella, Wolbachia, and Arsenophonus; Bartonella chomelii, Wolbachia spp., and Arsenophonus spp. were the dominant bacterial species in M. ovinus from Tibet, China. We also detected Kluyvera intermedia, Corynebacterium maris DSM 45190, Planomicrobium okeanokoites, and Rhodococcus erythropolis, of which the relative abundance of Kluyvera intermedia was high. Illumina Hiseq sequencing results demonstrated that 4 virus orders were detected in M. ovinus from Tibet, China, and 3 samples were annotated into 29 families, 30 families, and 28 families of viruses, respectively. Virus families related to vertebrates and insects mainly included Mimiviridae, Marseilleviridae, Poxviridae, Ascoviridae, Iridoviridae, Baculoviridae, Hytrosaviridae, Nudiviridae, Polydnaviridae, Adomaviridae, Asfarviridae, Hepeviridae, Herpesviridae, and Retroviridae; at the species level, the relative abundance of Tupanvirus_soda_lake, Klosneuvirus_KNV1, and Indivirus_ILV1 was higher. African swine fever virus and many poxviruses from the family Poxviridae were detected, albeit their relative abundance was low. The dominant bacterial phylum of M. ovinus from Tibet, China was Proteobacteria, and the dominant bacterial genera were Bartonella, Wolbachia, and Arsenophonus, where 23 out of 29 annotated bacteria genera were first reported in M. ovinus. Kluyvera intermedia, Corynebacterium maris DSM 45190, Planomicrobium okeanokoites, and Rhodococcus erythropolis were detected for the first time. All DNA viruses detected in this study have been reported in M. ovinus for the first time.

Temporal dynamics of oropharyngeal microbiome among SARS-CoV-2 patients reveals continued dysbiosis even after Viral Clearance

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic has posed multiple challenges to global public health. Clinical features and sequela of SARS-CoV-2 infection include long-term and short-term complications often clinically indistinguishable from bacterial sepsis and acute lung infection. Post-hoc studies of previous SARS outbreaks postulate secondary bacterial infections with microbial dysbiosis. Oral microbial dysbiosis, particularly the altered proportion of Firmicutes and Proteobacteria, observed in other respiratory virus infection, like influenza, has shown to be associated with increased morbidity and mortality. Oropharynx and lung share similar kinds of bacterial species. We hypothesized that alteration in the Human Oropharyngeal Microbiome in SARS-CoV-2 patients can be a clinical indicator of bacterial infection related complications. We made a longitudinal comparison of oropharyngeal microbiome of 20 SARS-CoV-2 patients over a period of 30 days; at three time points, with a 15 days interval; contrasting them with a matched group of 10 healthy controls. Present observation indicates that posterior segment of the oropharyngeal microbiome is a key reservoir for bacteria causing pneumonia and chronic lung infection on SARS-CoV-2 infection. Oropharyngeal microbiome is indeed altered and its α-diversity decreases, indicating reduced stability, in all SARS-CoV-2 positive individuals right at Day-1; i.e. within ~24 h of post clinical diagnosis. The dysbiosis persists long-term (30 days) irrespective of viral clearance and/or administration of antibiotics. There is a severe depletion of commensal bacteria phyla like Firmicutes among the patients and that depletion is compensated by higher proportion of bacteria associated with sepsis and severe lung infection from phyla Proteobacteria. We also found elevated proportions of certain genus that have previously been shown to be causal for lung pneumonia in studies of model organisms and human autopsies’ including Stenotrophomonas, Acenetobactor, Enterobactor, Klebsiella and Chryseobacterium that were to be elevated among the cases. We also show that responses to the antibiotics (Azithromycin and Doxycycline) are not uniform for all individuals.

Effect of Electrode Distances on Remediation of Eutrophic Water and Sediment by Sediment Microbial Fuel Cell Coupled Floating Beds.

Efficient and sustainable technologies for cleaning of contaminated water and sediments are in urgent demand. In this study, a new type of sediment microbial fuel cell coupled floating bed (FB-SMFC) was developed to repair eutrophic water and sediment in a cleaner way. The effect of electrode spacing on the power generation capacity and the synchronous remediation of pollutants from eutrophic water and sediment were studied. When the electrode distance was 60 cm, the maximum power generation and pollutant removal effects were obtained. At the end of the experiment, the maximum output voltage was 0.4 V, and the chemical oxygen demand (CODCr, potassium dichromate method), total nitrogen (TN), and total phosphorus (TP) contents in the overlying water were 8 mg/L, 0.7 mg/L, and 0.39 mg/L. The corresponding removal rates were 88.2%, 78.8%, and 59.0%, respectively. The removal rates of organic matter and TN in the sediment were 12.8% and 86.4%, respectively, and the fixation rate of TP was 29.2%. Proteobacteria was the dominant phylum of bacteria in the sediment and anode. Many anaerobic bacteria were found in the overlying water, which facilitated denitrification. Overall, the results of this research revealed a highly efficient and reliable strategy for eutrophic water and sediment remediation, aquatic ecosystems restoration, and human health protection.

Differences in intestinal microflora of birds among different ecological types

The intestinal microflora of animals plays a key role in metabolism, immunity, and development. Birds distributed across multiple ecological habitats. However, little is known about the differences in the intestinal microflora of birds among different ecological types. In this study, bird feces from different ecological types and orders were collected in Chongqing Zoo, China. In this study, high throughput sequencing of the 16S ribosomal RNA (rRNA) gene (amplicon sequencing) and metagenomics were used to analyze the composition and function differences of gut microbiota communities among different ecological types/orders. Firmicutes and Proteobacteria were the dominant bacteria phyla for all samples but there were significant differences in the α-diversity, community structure and microbial interactions between birds of different ecological types. The function differences involve most aspects of the body functions, especially for environmental information processing, organismal systems, human diseases, genetic information processing, and metabolism. These results suggest that diet and habitat are potential drivers of avian gut microbial aggregation. This preliminary study is of great significance for further research on the intestinal microflora of different ecological types of birds.

Correlation analysis between microbial diversity and physicochemical indices of Koumiss

This study examined the influence of change in microbial flora during fermentation on the quality of Koumiss. The microbial diversity of Koumiss samples was analyzed at different fermentation periods using high-throughput sequencing. Also, the physiochemical (protein, fat, ash, moisture, lactose, soluble solids, and energy) and functional (antioxidant activity, cholesterol removal ability, and bacteriostatic ability) indices were estimated. Finally, a correlation analysis was made between the change in microbial flora structure and physicochemical and functional indices. The dominant bacteria phylum was Firmicutes, and the dominant bacteria genus was Lactobacillus. In the early stage of fermentation, the dominant bacteria phylum of fresh mare milk was Actinobacteria, while the dominant bacteria genus was Rothia. Concerning fungal community structure, the dominant phylum was Ascomycota, and the dominant genus was Dekkera. In the early stage of fermentation too, the dominant fungal phylum was Ascomycota, but the dominant genus was Candida. The lactose and energy contents of fresh mare milk were higher, which was consistent with other physiochemical indices. After fermentation, the contents of lactose, soluble solids, and energy decreased, and the contents of protein and fat fluctuated. The functional characteristics of fermented mare milk are remarkable. Besides, it has a strong antibacterial ability. The bacteria that positively correlated with lactose, soluble solids, and energy were Rothia, Streptococcus, Enhydrobacter, and Macrococcus (p<0.05). Also, DPPH hydroxyl free radical capacity and reducing power positively correlated with Pichia (p < 0.05); Hydroxyl radical scavenging ability positively correlated with Yarrowia and Dipodascus (p < 0.05); Energy and lactose negatively correlated with Yarrowia and Dipodascus (p < 0.05).