The Impacts of Field Management on Soil and Tea Root Microbiomes

Due to the importance of microbes in soil health and crop production, manipulation of microbiomes provides a new strategy for improving crop growth and agricultural ecosystems. Current understanding is limited regarding the responses of soil and crop endophytic microbiomes to field management and microbiome programming. In this study, we investigated soil and tea root bacterial communities under conventional and organic cropping systems using 16S rRNA gene sequencing. A significant difference in soil and root bacterial community structure was observed under different field managements, leading to 43% and 35% variance, respectively. We also identified field management-sensitive species both in soils and tea roots that have great potential as bioindicators for bacterial microbiome manipulation. Moreover, through functional profile predictions of microbiomes, xenobiotics degradation in soil bacterial communities is enriched in organic farms, suggesting that biodegradation capabilities are enhanced under organic cropping systems. Our results demonstrate the effects of field management on both soil and tea root bacterial microbiomes and provide new insights into the reprogramming of microbial structures.

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Microbiome of Unilateral Chronic Rhinosinusitis: A Controlled Paired Analysis

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18189878 ◽

2021 ◽

Vol 18 (18) ◽

pp. 9878

Author(s):

Sang Chul Park ◽

Il-Ho Park ◽

Joong Seob Lee ◽

Sung Min Park ◽

Sung Hun Kang ◽

...

Keyword(s):

Chronic Rhinosinusitis ◽

Upper Airway ◽

16S Rrna Gene Sequencing ◽

Sinus Surgery ◽

Rrna Gene ◽

Upper Respiratory Tract ◽

Significant Difference ◽

Airway Microbiome ◽

Bacterial Microbiome ◽

Rrna Gene Sequencing

The sinonasal microbiota in human upper airway may play an important role in chronic rhinosinusitis (CRS). Thus, this study aimed to investigate the human upper airway microbiome in patients with unilateral CRS, and compare the sinonasal microbiome of the unilateral diseased site with that of a contralateral healthy site. Thirty samples, 15 each from the diseased and healthy sites, were collected from the middle meatus and/or anterior ethmoid region of 15 patients with unilateral CRS during endoscopic sinus surgery. DNA extraction and bacterial microbiome analysis via 16S rRNA gene sequencing were then performed. Corynebacterium showed the highest relative abundance, followed by Staphylococcus in samples from both the diseased and healthy sites. Further, the relative abundances of Staphylococcus and Pseudomonas were significantly lower in samples from diseased sites than in those from healthy sites. Conversely, anaerobes, including Fusobacterium, Bacteroides, and Propionibacterium, were abundantly present in samples from both sites, more so in samples from diseased sites. However, the sites showed no significant difference with respect to richness or diversity (p > 0.05). Our results indicate that CRS might be a polymicrobial infection, and also suggest that Corynebacterium and Staphylococcus may exist as commensals on the sinus mucosal surface in the upper respiratory tract.

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Analysis of bacterial communities associated with the benthic amphipodDiporeiain the Laurentian Great Lakes Basin

Canadian Journal of Microbiology ◽

10.1139/cjm-2014-0434 ◽

2015 ◽

Vol 61 (1) ◽

pp. 72-81 ◽

Cited By ~ 6

Author(s):

Andrew D. Winters ◽

Terence L. Marsh ◽

Travis O. Brenden ◽

Mohamed Faisal

Keyword(s):

Great Lakes ◽

Bacterial Communities ◽

Lake Michigan ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Great Lakes Basin ◽

The Past ◽

Significant Difference ◽

Rrna Gene Sequencing ◽

Extensive List

Bacterial communities play important roles in the biological functioning of crustaceans, yet little is known about their diversity, structure, and dynamics. This study was conducted to investigate the bacterial communities associated with the benthic amphipod Diporeia, an important component in the Great Lakes foodweb that has been declining over the past 3 decades. In this study, the combination of 16S rRNA gene sequencing and terminal restriction fragment length polymorphism revealed a total of 175 and 138 terminal restriction fragments (T-RFs) in Diporeia samples following treatment with the endonucleases HhaI and MspI, respectively. Relatively abundant and prevalent T-RFs were affiliated with the genera Flavobacterium and Pseudomonas and the class Betaproteobacteria. T-RFs affiliated with the order Rickettsiales were also detected. A significant difference in T-RF presence and abundance (P = 0.035) was detected among profiles generated for Diporeia collected from 4 sites in Lake Michigan. Comparison of profiles generated for Diporeia samples collected in 2 years from lakes Superior and Michigan showed a significant change in diversity for Lake Superior Diporeia but not Lake Michigan Diporeia. Profiles from one Lake Michigan site contained multiple unique T-RFs compared with other Lake Michigan Diporeia profiles, most notably one that represents the genus Methylotenera. This study generated the most extensive list of bacteria associated with Diporeia and sheds useful insights on the microbiome of Great Lakes Diporeia that may help to reveal potential causes of the decline of Diporeia populations.

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Diversity, Composition and Functional Inference of Gut Microbiota in Indian Cabbage white Pieris canidia (Lepidoptera: Pieridae)

Life ◽

10.3390/life10110254 ◽

2020 ◽

Vol 10 (11) ◽

pp. 254

Author(s):

Ying Wang ◽

Jianqing Zhu ◽

Jie Fang ◽

Li Shen ◽

Shuojia Ma ◽

...

Keyword(s):

Gut Microbiota ◽

16S Rrna Gene Sequencing ◽

Adult Survival ◽

Rrna Gene ◽

Life Stages ◽

Microbial Composition ◽

Significant Difference ◽

Functional Inference ◽

Rrna Gene Sequencing ◽

Insect Fitness

We characterized the gut microbial composition and relative abundance of gut bacteria in the larvae and adults of Pieris canidia by 16S rRNA gene sequencing. The gut microbiota structure was similar across the life stages and sexes. The comparative functional analysis on P. canidia bacterial communities with PICRUSt showed the enrichment of several pathways including those for energy metabolism, immune system, digestive system, xenobiotics biodegradation, transport, cell growth and death. The parameters often used as a proxy of insect fitness (development time, pupation rate, emergence rate, adult survival rate and weight of 5th instars larvae) showed a significant difference between treatment group and untreated group and point to potential fitness advantages with the gut microbiomes in P. canidia. These data provide an overall view of the bacterial community across the life stages and sexes in P. canidia.

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Deciphering Gut Microbiota Dysbiosis and Corresponding Genetic and Metabolic Dysregulation in Psoriasis Patients Using Metagenomics Sequencing

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.605825 ◽

2021 ◽

Vol 11 ◽

Author(s):

Shiju Xiao ◽

Guangzhong Zhang ◽

Chunyan Jiang ◽

Xin Liu ◽

Xiaoxu Wang ◽

...

Keyword(s):

Gut Microbiota ◽

Target Genes ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Phosphotransferase System ◽

Microbial Composition ◽

Kegg Pathways ◽

Significant Difference ◽

Rrna Gene Sequencing ◽

Endothelial Growth Factor

BackgroundIncreasing evidence has shown that alterations in the intestinal microbiota play an important role in the pathogenesis of psoriasis. The existing relevant studies focus on 16S rRNA gene sequencing, but in-depth research on gene functions and comprehensive identification of microbiota is lacking.ObjectivesTo comprehensively identify characteristic gut microbial compositions, genetic functions and relative metabolites of patients with psoriasis and to reveal the potential pathogenesis of psoriasis.MethodsDNA was extracted from the faecal microbiota of 30 psoriatic patients and 15 healthy subjects, and metagenomics sequencing and bioinformatic analyses were performed. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database, cluster of orthologous groups (COG) annotations, and metabolic analyses were used to indicate relative target genes and pathways to reveal the pathogenesis of psoriasis.ResultsCompared with healthy individuals, the gut microbiota of psoriasis patients displayed an alteration in microbial taxa distribution, but no significant difference in microbial diversity. A distinct gut microbial composition in patients with psoriasis was observed, with an increased abundance of the phyla Firmicutes, Actinobacteria and Verrucomicrobia and genera Faecalibacterium, Bacteroides, Bifidobacterium, Megamonas and Roseburia and a decreased abundance of the phyla Bacteroidetes, Euryarchaeota and Proteobacteria and genera Prevotella, Alistipes, and Eubacterium. A total of 134 COGs were predicted with functional analysis, and 15 KEGG pathways, including lipopolysaccharide (LPS) biosynthesis, WNT signaling, apoptosis, bacterial secretion system, and phosphotransferase system, were significantly enriched in psoriasis patients. Five metabolites, hydrogen sulfide (H2S), isovalerate, isobutyrate, hyaluronan and hemicellulose, were significantly dysregulated in the psoriatic cohort. The dysbiosis of gut microbiota, enriched pathways and dysregulated metabolites are relevant to immune and inflammatory response, apoptosis, the vascular endothelial growth factor (VEGF) signaling pathway, gut-brain axis and brain-skin axis that play important roles in the pathogenesis of psoriasis.ConclusionsA clear dysbiosis was displayed in the gut microbiota profile, genetic functions and relative metabolites of psoriasis patients. This study is beneficial for further understanding the inflammatory pathogenesis of psoriasis and could be used to develop microbiome-based predictions and therapeutic approaches.

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Mulching: A viable option to increase productivity of field and fruit crops

Journal of Applied and Natural Science ◽

10.31018/jans.v9i2.1306 ◽

2017 ◽

Vol 9 (2) ◽

pp. 974-982

Author(s):

Jagroop Kaur ◽

Harsimrat K. Bons

Keyword(s):

Soil Degradation ◽

Crop Production ◽

Cropping Systems ◽

Biological Activities ◽

Soil Health ◽

Underground Water ◽

Soil Productivity ◽

Fruit Crops ◽

Horticultural Crops ◽

Weed Growth

Mulching plays an important role in production of agricultural and horticultural crops in the current scenario of declining water table, soil degradation and climate change. The main objectives of mulching are to prevent loss of water by evaporation, prevention of soil erosion, weed control, to reduce fertilizer leaching, to promote soil productivity, to enhance yield and quality of field and fruit crops. So, mulching is useful to save our underground water resource, soil and environment for sustainable crop production. In this review paper, the literature clearly shows pronounced effects of mulching on soil health by improving the soil structure, soil fertility, biological activities, avoid soil degradation in addition to moisture conservation, regulating temperature, encouraging change in favourable micro-climate, check weed growth and ultimately increasing the productivity, quality, profitability and sustainability of crops and cropping systems irrespective of the system/situation.

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The Diversity of the Intestinal Flora Disturbed After Feeding Intolerance Recovery in Preterm Twins

Frontiers in Pediatrics ◽

10.3389/fped.2021.648979 ◽

2021 ◽

Vol 9 ◽

Author(s):

Ying Li ◽

Chunhong Jia ◽

Xiaojun Lin ◽

Lili Lin ◽

Lizhen Li ◽

...

Keyword(s):

Acid Metabolism ◽

Intestinal Flora ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Feeding Intolerance ◽

Fecal Samples ◽

Kegg Pathways ◽

Intestinal Bacterial Community ◽

Β Diversity ◽

Significant Difference

Background: Feeding intolerance (FI) is a common condition in premature infants that results in growth retardation and even necrotizing enterocolitis. The gut microbiome is linked to FI occurrence; however, the outcome after FI recovery is unclear.Methods: Fecal samples were collected from 11 pairs of premature twins/triplets for 16S rRNA gene sequencing. Initial fecal samples were collected shortly after admission, and then every other week until 7 weeks or discharge.Results: After FI recovery, there was no significant difference in the β-diversity of the intestinal flora between the FI group and the feeding tolerance (FT) group. By contrast, there was a significant difference in the β-diversity. Proteobacteria was the predominant phylum in the microbiome of the FI group, whereas Firmicutes was the predominant phylum in the microbiome of the FT group. The predominant bacteria with LDA >4 between the two groups at 13–15 days after birth, 19–28 days after birth, and at discharge were different, with the proportions of Bacillus, Clostridium butyricum, and Clostridium being highest in the FT group and Firmicutes, unidentified_Clostridiales, and Proteobacteria being highest in the FI group. Similarly, there were significant differences in the relative abundances of KEGG pathways, such as fatty acid metabolism, DNA repair and recombination proteins, energy metabolism, and amino acid metabolism, between the two groups (P < 0.01).Conclusions: There was a significant difference in diversity of the intestinal flora after feeding intolerance recovery. Feeding intolerance may disturb the succession of the intestinal bacterial community.

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Interplay between Fungal Infection and Bacterial Associates in the Wax Moth Galleria mellonella under Different Temperature Conditions

Journal of Fungi ◽

10.3390/jof6030170 ◽

2020 ◽

Vol 6 (3) ◽

pp. 170

Author(s):

Vadim Yu Kryukov ◽

Elena Kosman ◽

Oksana Tomilova ◽

Olga Polenogova ◽

Ulyana Rotskaya ◽

...

Keyword(s):

Fungal Infection ◽

Bacterial Communities ◽

Galleria Mellonella ◽

Fungal Growth ◽

16S Rrna Gene Sequencing ◽

Illumina Miseq ◽

Rrna Gene ◽

Cultivable Bacteria ◽

Stress Related Genes ◽

Rrna Gene Sequencing

Various insect bacterial associates are involved in pathogeneses caused by entomopathogenic fungi. The outcome of infection (fungal growth or decomposition) may depend on environmental factors such as temperature. The aim of this study was to analyze the bacterial communities and immune response of Galleria mellonella larvae injected with Cordyceps militaris and incubated at 15 °C and 25 °C. We examined changes in the bacterial CFUs, bacterial communities (Illumina MiSeq 16S rRNA gene sequencing) and expression of immune, apoptosis, ROS and stress-related genes (qPCR) in larval tissues in response to fungal infection at the mentioned temperatures. Increased survival of larvae after C. militaris injection was observed at 25 °C, although more frequent episodes of spontaneous bacteriosis were observed at this temperature compared to 15 °C. We revealed an increase in the abundance of enterococci and enterobacteria in the midgut and hemolymph in response to infection at 25 °C, which was not observed at 15 °C. Antifungal peptide genes showed the highest expression at 25 °C, while antibacterial peptides and inhibitor of apoptosis genes were strongly expressed at 15 °C. Cultivable bacteria significantly suppressed the growth of C. militaris. We suggest that fungi such as C. militaris may need low temperatures to avoid competition with host bacterial associates.

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Effect of bamboo vinegar powder as an antibiotic alternative on the digesta bacteria communities of finishing pigs

Canadian Journal of Microbiology ◽

10.1139/cjm-2018-0058 ◽

2018 ◽

Vol 64 (10) ◽

pp. 732-743

Author(s):

Huan Qu ◽

Yanjie Huang ◽

Yinghao Shi ◽

Ying Liu ◽

Shenglong Wu ◽

...

Keyword(s):

Bacterial Communities ◽

Metabolic Pathways ◽

Growth And Development ◽

Intestinal Microflora ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Finishing Pigs ◽

Rrna Gene Sequencing ◽

Bacteria Communities

This study investigated the use for bamboo vinegar powder as an antibiotic alternative in the diet of growing–finishing pigs by examining their digestive bacterial communities. Forty-five Duroc × Landrace × Yorkshire growing–finishing pigs were randomly allocated to five diet groups: 0%, 0.5%, 1.0%, or 1.5% bamboo vinegar levels and antibiotics. After 37 days, the digesta in duodenum of four pigs from each treatment were analyzed for their bacterial community compositions using 16S rRNA gene sequencing. The addition of 1.5% bamboo vinegar powder had an effect on the intestinal microflora most similar to that of antibiotics, indicating its potential to promote the growth and development of finishing pigs. We also found the 1.5% bamboo vinegar powder group to have an increased abundance of Firmicutes/Bacteroidetes compared with the other bamboo vinegar powder groups, which may enhance the ability of the host to absorb food energy and store more body fat. Additionally, the effects of bamboo vinegar powder on promoting the abundances of Lactobacillus and Thalassospira and on inhibiting Streptococcus and Prevotella growth revealed it may play an important role in animal production. Moreover, functional predictions of microbes via PICRUSt indicated that feed supplemented with 1.5% bamboo vinegar powder could promote many vital metabolic pathways.

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Loss of bacterial diversity in the sinuses is associated with lower smell discrimination scores

Scientific Reports ◽

10.1038/s41598-020-73396-3 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Kristi Biswas ◽

Brett Wagner Mackenzie ◽

Charlotte Ballauf ◽

Julia Draf ◽

Richard G. Douglas ◽

...

Keyword(s):

Bacterial Diversity ◽

Bacterial Communities ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Olfactory Dysfunction ◽

Rrna Gene ◽

Olfactory Loss ◽

Olfactory Impairment ◽

Rrna Gene Sequencing ◽

Normal Sense

Abstract Olfactory impairment affects ~ 20% of the population and has been linked to various serious disorders. Microbes in the nasal cavity play a key role in priming the physiology of the olfactory epithelium and maintaining a normal sense of smell by the host. The aim of this study was to explore the link between olfactory dysfunction and nasal bacterial communities. A total of 162 subjects were recruited for this study from a specialized olfactory dysfunction clinic and placed into one of three groups: anosmia, hyposmia or normosmia. Swabs from the nasal middle meatus were collected from each subject then processed for bacterial 16S rRNA gene sequencing. No overall differences in bacterial diversity or composition were observed between the three cohorts in this study. However, the relative abundances of Corynebacterium spp. and Streptococcus spp. were significantly (p < 0.05) different in subjects with olfactory loss. Furthermore, subjects with deficiencies in discriminating between smells (based on discrimination scores) had a lower bacterial diversity (Simpson’s evenness p < 0.05). While these results are preliminary in nature, potential bacterial biomarkers for olfactory loss were identified. These findings need to be further validated and biologically tested in animal models.

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Heliconius Butterflies Host Characteristic and Phylogenetically Structured Adult-Stage Microbiomes

Applied and Environmental Microbiology ◽

10.1128/aem.02007-20 ◽

2020 ◽

Vol 86 (24) ◽

Cited By ~ 1

Author(s):

Tobin J. Hammer ◽

Jacob C. Dickerson ◽

W. Owen McMillan ◽

Noah Fierer

Keyword(s):

Bacterial Communities ◽

Evolutionary Biology ◽

Adult Stage ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Phylogenetic Structure ◽

Shotgun Metagenomics ◽

Microbiome Composition ◽

Form And Function ◽

Passion Vine

ABSTRACT Lepidoptera (butterflies and moths) are diverse and ecologically important, yet we know little about how they interact with microbes as adults. Due to metamorphosis, the form and function of their adult-stage microbiomes might be very different from those of microbiomes in the larval stage (caterpillars). We studied adult-stage microbiomes of Heliconius and closely related passion-vine butterflies (Heliconiini), which are an important model system in evolutionary biology. To characterize the structure and dynamics of heliconiine microbiomes, we used field collections of wild butterflies, 16S rRNA gene sequencing, quantitative PCR, and shotgun metagenomics. We found that Heliconius butterflies harbor simple and abundant bacterial communities that are moderately consistent among conspecific individuals and over time. Heliconiine microbiomes also exhibited a strong signal of the host phylogeny, with a major distinction between Heliconius and other butterflies. These patterns were largely driven by differing relative abundances of bacterial phylotypes shared among host species and genera, as opposed to the presence or absence of host-specific phylotypes. We suggest that the phylogenetic structure in heliconiine microbiomes arises from conserved host traits that differentially filter microbes from the environment. While the relative importance of different traits remains unclear, our data indicate that pollen feeding (unique to Heliconius) is not a primary driver. Using shotgun metagenomics, we also discovered trypanosomatids and microsporidia to be prevalent in butterfly guts, raising the possibility of antagonistic interactions between eukaryotic parasites and colocalized gut bacteria. Our discovery of characteristic and phylogenetically structured microbiomes provides a foundation for tests of adult-stage microbiome function, a poorly understood aspect of lepidopteran biology. IMPORTANCE Many insects host microbiomes with important ecological functions. However, the prevalence of this phenomenon is unclear because in many insect taxa, microbiomes have been studied in only part of the life cycle, if at all. A prominent example is butterflies and moths, in which the composition and functional role of adult-stage microbiomes are largely unknown. We comprehensively characterized microbiomes in adult passion-vine butterflies. Butterfly-associated bacterial communities are generally abundant in guts, consistent within populations, and composed of taxa widely shared among hosts. More closely related butterflies harbor more similar microbiomes, with the most dramatic shift in microbiome composition occurring in tandem with a suite of ecological and life history traits unique to the genus Heliconius. Butterflies are also frequently infected with previously undescribed eukaryotic parasites, which may interact with bacteria in important ways. These findings advance our understanding of butterfly biology and insect-microbe interactions generally.

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