Metagenomic analysis decodes the fungal diversity  of bio-dynamic preparations

Aim: Biodynamic farming system involves use of 8 different biodynamic preparations (BD 500-BD 507). Multi functionality of any ecosystem is due to its microbial diversity and community composition of microbes. So the present study was aimed to determine the total fungal population viz. unculturable ones, metagenomic analysis was done. Methodology: In the present study, 18S rDNA sequencing of V3-V4 amplicon regions was performed to identify and characterize fungal diversity, which existed in these preparations. Results: Alpha diversity was found to be maximum in BD506 with 868 OTU (operational taxanomic units) and minimum in BD507 with 254 OTU. At phylum level, the most abundant phylum was Ascomycota as recorded in 7 BD preparations with exception in the BD 500 (Unassigned). At genus level highest percentage of OTU abundance was observed for unassigned genus in all BD preparations, except Mortierella in BD 500 and BD 502; Microascus in BD 501 and BD504; Gymnoascus in BD503, Scedosporium in BD 505, Mucor in BD 506 and Hyphopichia in BD 507. On the basis of species diversity, BD502, 503 and 506 showed high percentage of OTU abundance for Mucor racemosus, while Mortierella oligospora was abundant in BD500, Dipodascus geotrichum in BD 501, Kernia pachypleura in BD504, Petriella setifera in BD505 and Hyphopichia burtonii in BD 507. Interpretation: This indicated a unqiue class of fungus predominating each type of BD preparation. Furthermore, a large proportion of unassigned fungi at phylum and genus level were detected in metagenome analysis which might have specific roles in contributing for their overall effectiveness of each kind of BD preparations.

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The plant secondary compound swainsonine reshapes gut microbiota in plateau pikas (Ochotona curzoniae)

Applied Microbiology and Biotechnology ◽

10.1007/s00253-021-11478-6 ◽

2021 ◽

Author(s):

Shien Ren ◽

Chao Fan ◽

Liangzhi Zhang ◽

Xianjiang Tang ◽

Haibo Fu ◽

...

Keyword(s):

Gut Microbiota ◽

Artificial Diet ◽

Alpha Diversity ◽

Term Treatment ◽

Short Term Treatment ◽

Ochotona Curzoniae ◽

Rdna Sequencing ◽

Long Term Treatment ◽

Significant Difference ◽

Herbivorous Mammals

Abstract Plants produce various plant secondary compounds (PSCs) to deter the foraging of herbivorous mammals. However, little is known about whether PSCs can reshape gut microbiota and promote gut homeostasis of hosts. Using 16S rDNA sequencing to investigate the effects of PSCs on the gut microbiota of small herbivorous mammals, we studied plateau pikas (Ochotona curzoniae) fed diets containing swainsonine (SW) extracted from Oxytropis ochrocephala. Our results showed that both long- and short-term treatment of a single artificial diet in the laboratory significantly reduced alpha diversity and significantly affected beta diversity, core bacteria abundance, and bacterial functions in pikas. After SW was added to the artificial diet, the alpha diversity significantly increased in the long-term treatment, and core bacteria (e.g., Akkermansiaceae) with altered relative abundances in the two treatments showed no significant difference compared with pikas in the wild. The complexity of the co-occurrence network structure was reduced in the artificial diet, but it increased after SW was added in both treatments. Further, the abundances of bacteria related to altered alanine, aspartate, and glutamate metabolism in the artificial diet were restored in response to SW. SW further decreased the concentration of short-chain fatty acids (SCFAs) in both treatments. Our results suggest that PSCs play a key role in regulating gut microbiota community and intestinal homeostasis, thereby maintaining host health. Key points • Swainsonine improves the intestinal bacterial diversity of plateau pikas. • Swainsonine promotes the recovery of core bacterial abundances in the gut of plateau pikas. • Swainsonine promotes the restoration of intestinal bacterial functions of plateau pikas.

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PSVII-9 Influence of lactose and milk oligosaccharides in whey permeate on jejunal mucosa-associated microbiota in nursery pigs during 7 to 11 kg BW

Journal of Animal Science ◽

10.1093/jas/skab235.732 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 407-407

Author(s):

Ki Beom Jang ◽

Sung Woo Kim

Keyword(s):

Alpha Diversity ◽

Jejunal Mucosa ◽

16S Rdna Sequencing ◽

Sequencing Data ◽

Milk Oligosaccharides ◽

Whey Permeate ◽

Nursery Pigs ◽

Rdna Sequencing ◽

Acid Producing Bacteria ◽

Diversity Estimates

Abstract This study aimed to evaluate supplemental effects of milk carbohydrates in whey permeate on jejunal mucosa-associated microbiota in nursery pigs during 7 to 11 kg BW. A total of 720 pigs at 7.5 kg BW were allotted to 6 treatments (6 pens/treatment and 20 pigs/pen). Treatments were 6 levels of whey permeate supplementation (0, 3.75, 7.50, 11.25, 15.00, and 18.75%) and fed to pigs for 11 d. On d 11, 36 pigs representing median BW of each pen were euthanized to collect the jejunal mucosa to evaluate microbiota in the jejunum by 16S rDNA sequencing. Data were analyzed using contrasts in MIXED procedure of SAS. Whey permeate contained 76.3% lactose and 0.4% milk oligosaccharides. Increasing whey permeate supplementation from 0 to 18.75% did not affect the alpha-diversity estimates of microbiota. Whey permeate supplementation tended to decrease (P = 0.073, 1.59 to 1.22) Firmicutes:Bacteroidetes compared with no addition of whey permeate. Increasing whey permeate supplementation tended to linearly increase Bifidobacteriaceae (P = 0.089, 0.73 to 1.11), decrease Enterobacteriaceae (P = 0.091, 1.04 to 0.52), decrease Stretococcaceae (P = 0.094, 1.50 to 0.71), and caused quadratic changes (P < 0.05) on Lactobacillaceae (maximum: 9.14% at 12.91% whey permeate). Increasing whey permeate supplementation caused a quadratic change (P < 0.05) on Lactobacillus_Salivarius (maximum: 0.92% at 7.35% whey permeate) and tended to cause quadratic changes on Lactobacillus_Rogosae (P = 0.083; maximum: 0.53% at 8.45% whey permeate) and Lactobacillus_Mucosae (P = 0.092; maximum: 0.70% at 6.98% whey permeate). In conclusion, supplementation of whey permeate as sources of lactose and milk oligosaccharides at a range from 7 to 13% seems to be beneficial to nursery pigs by increasing the abundance of lactic acid-producing bacteria in the jejunal mucosa.

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An interventional Soylent diet increases the Bacteroidetes to Firmicutes ratio in human gut microbiome communities: a randomized controlled trial

10.1101/200881 ◽

2017 ◽

Cited By ~ 1

Author(s):

Ryan H. Hsu ◽

Dylan M. McCormick ◽

Mitchell J. Seitz ◽

Lauren M. Lui ◽

Harneet S. Rishi ◽

...

Keyword(s):

Gut Microbiome ◽

Intestinal Inflammation ◽

Controlled Trial ◽

Alpha Diversity ◽

Diet Group ◽

Positive Health ◽

Unifrac Distance ◽

Liquid Meal ◽

Regular Diet ◽

Rdna Sequencing

AbstractOur knowledge of the relationship between the gut microbiome and health has rapidly expanded in recent years. Diet has been shown to have causative effects on microbiome composition, which can have subsequent implications on health. Soylent 2.0 is a liquid meal replacement drink that satisfies nearly 20% of all recommended daily intakes per serving. This study aims to characterize the changes in gut microbiota composition resulting from a short-term Soylent diet. Fourteen participants were separated into two groups: 5 in the regular diet group and 9 in the Soylent diet group. The regular diet group maintained a diet closely resembling self-reported regular diets. The Soylent diet group underwent three dietary phases: A) a regular diet for 2 days, B) a Soylent-only diet (five servings of Soylent daily and water as needed) for 4 days, and C) a regular diet for 4 days. Daily logs self-reporting diet, Bristol stool ratings, and any abdominal discomfort were electronically submitted. Eight fecal samples per participant were collected using fecal sampling kits, which were subsequently sent to uBiome, Inc. for sample processing and V4 16S rDNA sequencing. Reads were clustered into operational taxonomic units (OTUs) and taxonomically identified against the GreenGenes 16S database. We find that an individual’s alpha-diversity is not significantly altered during a Soylent-only diet. In addition, principal coordinate analysis using the unweighted UniFrac distance metric shows samples cluster strongly by individual and not by dietary phase. Among Soylent dieters, we find a significant increase in the ratio of Bacteroidetes to Firmicutes abundance, which is associated with several positive health outcomes, including reduced risks of obesity and intestinal inflammation.

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Fecal microbiota transplantation increases colonic IL-25 and dampens tissue inflammation in patients with recurrent Clostridioides difficile

10.1101/2021.07.16.21260643 ◽

2021 ◽

Author(s):

Ning-Jiun Jan ◽

Noah Oakland ◽

Pankaj Kumar ◽

Girija Ramakrishnan ◽

Brian W. Behm ◽

...

Keyword(s):

Mononuclear Cells ◽

Fecal Microbiota Transplantation ◽

Alpha Diversity ◽

The United States ◽

Fecal Microbiota ◽

Peripheral Blood Mononuclear ◽

Clostridioides Difficile ◽

Rdna Sequencing ◽

Clostridioides Difficile Infection ◽

The Impact

Background: Clostridioides difficile infection (CDI) is the most common hospital-acquired infection in the United States. Antibiotic-induced dysbiosis is the primary cause of susceptibility and fecal microbiota transplantation (FMT) has emerged as an effective therapy for recurrence. We previously demonstrated in the mouse model of CDI that antibiotic-induced dysbiosis reduced colonic expression of IL-25, and that FMT protected in part by restoring gut commensal bacteria-mediated IL-25 signaling. Here we conducted a prospective clinical trial to test the impact of FMT on immunity, specifically testing in humans if FMT induced IL-25 expression in the colon. Methods: Subjects received colonic biopsies and blood sampling at the time of FMT and 60-days later. Colon biopsies were assayed for IL-25 by immunoassay, for mRNA by RNAseq, and for bacterial content by 16 S rDNA sequencing. High dimensional flow cytometry was also conducted on peripheral blood mononuclear cells pre- and post-FMT. Results: All 10 subjects who received FMT had no CDI recurrences over a 2 year follow-up post FMT. FMT increased alpha diversity of the colonic microbiota and was associated with several immunologic changes. The cytokine IL-25 was increased in colonic tissue. In addition, increased expression of homeostatic genes and repression of inflammatory genes was observed in colonic mRNA transcripts. Finally, circulating Th17 cells were decreased post-FMT. Conclusion: The increase in the cytokine IL-25 accompanied by decreased inflammation is consistent with FMT acting in part to protect from recurrent CDI via restoration of commensal activation of type 2 immunity.

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Responses of Rhizosphere Fungal Communities to the Sewage Sludge Application into the Soil

Microorganisms ◽

10.3390/microorganisms7110505 ◽

2019 ◽

Vol 7 (11) ◽

pp. 505 ◽

Cited By ~ 2

Author(s):

Katarína Ondreičková ◽

Marcela Gubišová ◽

Michaela Piliarová ◽

Miroslav Horník ◽

Pavel Matušinský ◽

...

Keyword(s):

Sewage Sludge ◽

Fungal Community ◽

18S Rdna ◽

Mycorrhizal Fungi ◽

Fungal Diversity ◽

Municipal Wastewater ◽

Environmental Changes ◽

Community Diversity ◽

Rdna Sequencing ◽

Sludge Application

Due to the increasing sewage sludge production in the world and problems with its disposal, an application of sludge to the soil appears to be a suitable solution considering its fertilizer properties and ability to improve the soil physical conditions. On the other hand, the sludge may also contain undesirable and toxic substances. Since soil microorganisms are sensitive to environmental changes, they can be used as indicators of soil quality. In this study, we used sewage sludge (SS) from two municipal wastewater treatment plants (SS-A and SS-B) in the dose of 5 t/ha and 15 t/ha in order to determine possible changes in the fungal community diversity, especially arbuscular mycorrhizal fungi (AMF), in the rhizosphere of Arundo donax L. Rhizosphere samples were collected in summer and autumn for two consecutive years and the fungal diversity was examined using terminal restriction fragment length polymorphism and 18S rDNA sequencing. Fungal alpha diversity was more affected by SS-A than SS-B probably due to the higher heavy metal content. However, based on principal component analysis and ANOSIM, significant changes in overall fungal diversity were not observed. Simultaneously, 18S rDNA sequencing showed that more various fungal taxa were detected in the sample with sewage sludge than in the control. Glomus sp. as a representative of AMF was the most represented. Moreover, Funneliformis in both samples and Rhizophagus in control with Septoglomus in the sludge sample were other representatives of AMF. Our results indicate that the short-term sewage sludge application into the soil does not cause a shift in the fungal community composition.

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Field Fungal Diversity in Freshly Harvested Maize

International Journal of Biochemistry Research & Review ◽

10.9734/ijbcrr/2019/v26i130088 ◽

2019 ◽

pp. 1-13 ◽

Cited By ~ 1

Author(s):

Xiang Dong Sun ◽

Hong Shan ◽

Lili Li ◽

Ping Su ◽

Jing Lan ◽

...

Keyword(s):

Human Health ◽

Fungal Diversity ◽

Fungal Species ◽

Heilongjiang Province ◽

Maize Production ◽

Genus Level ◽

Dominant Classes ◽

Growth And Reproduction

Maize is a major crop in China and maize production in Heilongjiang Province ranks No.1 in the country in annual maize production in the whole country. Maize is prone to invasion by fungi and mycotoxins produced by these fungi are proven to be serious threats to animals as well as human health. Through high through-put sequencing we detected the dominant phylum to be Ascomycota; Dothideomycetes, Sordariomycetes, Eurotiomycetes and Tremellomycetes, Saccharomycetes were the dominant classes; Hypocreales, Eurotiales, Capnodiales, Saccharomycetales, Tremellales, and Pleosporales were the main orders; Nectriaceae, Trichocomaceae, Cladosporiaceae, Debaryomycetaceae, Tremellaceae, and Pleosporaceae were major families; Gibberella, Cladosporium, Papiliotrema, Penicillium, Scheffersomyces, Talaromyces, and Epicoccum were the most abundant phylotypes at the genus level. Epicoccum_nigrum, Gibberella_zeae, Papiliotrema_flavescens, and Scheffersomyces_shehatae were the dominant fungal species. Great fungal diversity was observed in the maize samples harvested in the five major maize-growing regions in Heilongjiang Province. Maize-1 in Nenjiang County was observed to have the greatest fungal diversity and abundance among the five regions. Since some of the fungal species are mycotoxin producing, it is necessary to take precautions to ensure the maize is stored under safe conditions to prevent the occurrence of mycotoxins and the growth and reproduction of other fungi which results in deterioration in the quality of maize.

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Microbiome Analysis of Gut Bacterial Communities of Healthy and Diseased Malaysian Mahseer (Tor tambroides)

10.1101/2021.12.08.471852 ◽

2021 ◽

Author(s):

Melinda Mei Lin Lau ◽

Cindy Jia Yung Kho ◽

LEONARD WHYE KIT LIM ◽

Siew Chuiang Sia ◽

Hung Hui Chung ◽

...

Keyword(s):

Gut Microbiota ◽

Bacterial Communities ◽

Alpha Diversity ◽

Microbiota Composition ◽

Petechial Haemorrhage ◽

Rdna Sequencing ◽

Degrading Bacteria ◽

And Function ◽

Gut Microbial Community ◽

Gut Microbiota Composition

Aims: The gut microbiota is referred to an extra organ and is ciritical in assisting the host in terms of nutrition and immunity. Environmental stressors could alter gut microbial community and cause gut inflammation. This study aimed to investigate and compare the gut microbiota community between healthy and diseased Tor tambroides. Methodology and results: In this study, such gut microbial alterations were explored using NGS-based 16S rDNA sequencing on the Malaysian mahseer (T. tambroides). Three adult healthy and three diseased adult Malaysian mahseers (showing signs of exophthalmia, coelomic distension and petechial haemorrhage) were obtained from LTT Aquaculture Sdn Bhd. Our results revealed significant differences in microbial diversity, composition and function between both populations of T. tambroides. Alpha diversity analysis depicts lower diversity of gut microbiota composition in diseased T. tambroides as compared to the healthy group. In particular, Enterobacteriaceae, Aeromonas, Bacteroides, Vibrio and Pseudomonas were found within gut microbiota of the diseased fishes. In addition, cellulose-degrading bacteria and protease-producing bacteria were identified from the gut of T. tambroides. Conclusion, significance and impact of study: Thus, our findings emphasised on the association between the alteration in gut microbiota composition and infectious abdominal dropsy (IAD) in T. tambroides. This finding is important to provide basic information for further diagnosis, prevention and treatment of intestinal diseases in fish.

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MALDI-TOF Mass Spectrometry Fingerprinting Performance Versus 16S rDNA Sequencing to Identify Bacterial Microflora From Seafood Products and Sea Water Samples

Frontiers in Marine Science ◽

10.3389/fmars.2021.650116 ◽

2021 ◽

Vol 8 ◽

Author(s):

Thomas Brauge ◽

Sylvain Trigueros ◽

Arnaud Briet ◽

Sabine Debuiche ◽

Guylaine Leleu ◽

...

Keyword(s):

Mass Spectrometry ◽

16S Rdna ◽

Sea Water ◽

Species Level ◽

16S Rdna Sequencing ◽

Genus Level ◽

Maldi Tof ◽

Rdna Sequencing ◽

Seafood Products ◽

Tof Ms

We evaluated the performance of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) associated with the Bruker BioTyperTM V7.0.0 database for the identification of 713 bacterial strains isolated from seafood products and sea water samples (ANSES B3PA collection) under culture conditions that may have been significantly different from those used to create the reference spectrum vs. the 16S rDNA sequencing. We identified 78.8% of seafood isolates with 46.7% at the species level (Bruker score above 2) and 21.2% (Bruker score between 1.7 and 2) at the genus level by the two identification methods, except for 3.8% of isolates with a difference of identification between the two methods (Bruker score between 1.7 and 2). There were 41.9% isolates (Bruker score below 1.7) with the identification at the genus level. We identified 94.4% of seafood isolates with 16S rDNA sequencing. The MALDI-TOF allowed a better strain identification to the species level contrary to the 16s rDNA sequencing, which allowed an identification mainly to the genus level. MALDI-TOF MS in association with the Bruker database and 16S rDNA sequencing are powerful tools to identify a wide variety of bacteria from seafood but require further identification by biochemical, molecular technique or other conventional tests.

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Metagenome Techniques for Detection of Pathogens Causing Ocular Infection

Reports ◽

10.3390/reports4010006 ◽

2021 ◽

Vol 4 (1) ◽

pp. 6

Author(s):

Tatsuhiko Kobayashi ◽

Takashi Suzuki ◽

Yukinobu Okajima ◽

Kotaro Aoki ◽

Yoshikazu Ishii ◽

...

Keyword(s):

Illumina Miseq ◽

Metagenomic Analysis ◽

Ocular Infection ◽

Fungal Culture ◽

Metagenomic Sequencing ◽

Viral Pathogens ◽

Metagenome Analysis ◽

Ocular Infections ◽

Shotgun Metagenomic Sequencing ◽

Corneal Scraping

Metagenomic analysis is the comprehensive study of DNA using clinical specimens of organisms including bacteria, fungi, and viruses. In this study, we investigated the efficacy of metagenomic analysis for diagnosing ocular infections, including 11 keratitis cases, four iridocyclitis cases, and one endophthalmitis case. Corneal scraping, aqueous humor, and vitreous humor, were collected respectively. Ocular specimens were used for bacterial and fungal culture, and PCR for detecting viral DNA. Shotgun metagenomic sequencing for 150 bases of single end was performed by Illumina MiSeq® System. Sequence was retrieved from the database at NCBI using a MegaBLAST search. Since Propionibacterium spp. are commensal bacteria found at the ocular surface, they were excluded from analysis. Six cases (37.5%) were positive for culture or PCR. Metagenome techniques revealed that 9 cases (56.3%) included genomes of organisms that were considered pathogenic in specimens. Five cases (31.3%) possessed genomes of organisms like themselves that were detected by culture and PCR. Six cases (37.5%) were negative for culture, PCR, and metagenome analysis. Moreover, viral pathogens (HSV-1, 2 cases; and VZV, 1 case) were detected by only metagenome analysis. Metagenome analysis using an ocular sample can detect microbial genome comprehensively, and viral pathogens, which were not detected by conventional examination.

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Unraveling metabolically active fungal-bacterial diversity in commercial organic vineyard soils

10.5194/egusphere-egu2020-18343 ◽

2020 ◽

Author(s):

Carmen Biel ◽

Miriam Guivernau ◽

Marc Viñas ◽

Xavier Aranda ◽

Felicidad de Herralde

Keyword(s):

Bacterial Diversity ◽

Fungal Diversity ◽

Sandy Loam ◽

Soil Depth ◽

Sequencing Analysis ◽

Fungal Population ◽

Post Harvest ◽

Bloom Period ◽

Vineyard Soils ◽

The Impact

This study aims to assess the impact of the pre-bloom and post-harvest periods on the diversity of metabolically active soil-rhizosphere microbiota in a commercial vineyard in Sant Sadurn&#237; d&#8217;Anoia, a typical wine producing region (Pened&#232;s DO, Catalonia, Spain). Thereby, total genomic DNA and RNA was simultaneously monitored to distinguish total from active bacterial-fungal microbiota, by molecular tools in both periods. The studied organic vineyard had 20 years old plants of the white grape variety of Macabeu and 41B as a rootstock. Soil had last been amended (14 tm/ha of composted cow manure) 5 years before.The soil was monitored in April 2018 in the pre-bloom period (stages 09 to 12 Eichhorn and Lorenz 1977) and the post-harvest period (October 2018) in 2 different plots of the vineyard: Zone1 (loam texture with permanent cover crop) and Zone 4 (sandy-loam without vegetal cover). Samples soils were obtained at a soil depth of30 cm and 20 cm of distance from a plant (n=4 for each plot and sampling event). Each soil sample was submerged in a DNA/RNA preservative solution at 4&#8304;C and afterward stored at -20&#8304;C until the further analysis. In order to quantify and to assess bacterial and fungal diversity (total and active), (RT)qPCR and MiSeq-Illumina analysis (16SrRNA/ITS1rRNA region) were performed.Results showed that in post-harvest period the bacterial populations were more active in both zones (2 and 5 orders of magnitude in Zone1 and Zone4, respectively) vs. pre-bloom period. Metabolically active fungal population was increased in both plots by 4 orders of magnitude. It is noteworthy to mention that fungal population was present but not active in pre-harvest period. This fact could be explained for the mutualistic microbe interaction and the environmental conditions (soil temperature and soil water content), including grape drop in harvest linked to rainy conditions.High-throughput sequencing analysis revealed that the microbial diversity was specific for each plot, vine and sampling period. Bacterial population in post-harvest was more diversified but still dominated by Actinobacteria (mainly by Actinomycetales order), Proteobacteria (mainly by Rhizobiales and Pseudomonadales orders). Interestingly, during post-harvest Clostridiales (Firmicutes phylum), present in the pre-bloom period, completely disappeared. Alpha bacterial diversity was higher than fungal one in both plots. Interestingly, the bacterial diversity (H Shannon index) of metabolically active bacteria (cDNA) was higher during post-harvest season compared to April, suggesting more activity and diversity in the former. On the contrary, fungal diversity was smaller and less uniform in both periods. They were predominated by Ascomycota, Basidiomycota and Zygomycota phyla. Noticeably, the relative abundance (RA) of existing fungal population (DNA) in the soil were highly different compared to the RA of active fungal community (cDNA).In conclusion, simultaneous RNA/DNA-based molecular biology tools could improve the knowledge of metabolically active microbial populations in vineyard soils under different seasons.Funding: VITIMPAC project (INIA RTA2015-00091-00-00).

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