scholarly journals Genomes of keystone Mortierella species lead to better in silico prediction of soil mycobiome functions from Taiwan's offshore islands

2021 ◽  
Author(s):  
Yu-fei Lin ◽  
Wei-An Liu ◽  
Yu-Ching Liu ◽  
Hsin-Han Lee ◽  
Yen-Ju Lin ◽  
...  
Keyword(s):  
Island Biogeography ◽  
Functional Relationship ◽  
Gene Prediction ◽  
Amplicon Sequencing ◽  
Island Size ◽  
Network Analyses ◽  
Operational Taxonomic Units ◽  
Geographical Separation ◽  
Zero Radius ◽  
Geographical Distances

The ability to correlate the functional relationship between microbial communities and their environment is critical to understanding microbial ecology. There is emerging knowledge on island biogeography of microbes but how island characteristics influence functions of microbial community remain elusive. Here, we explored soil mycobiomes from nine islands adjacent to Taiwan using ITS2 amplicon sequencing. Geographical distances and island size were positively correlated to dissimilarity in mycobiomes, and we identified 56 zero-radius operational taxonomic units (zOTUs) that were ubiquitously present across all islands, and as few as five Mortierella zOTUs dominate more than half of mycobiomes. Correlation network analyses revealed that seven of the 45 hub species were part of the ubiquitous zOTUs belonging to Mortierella, Trichoderma, Aspergillus, Clonostachys and Staphylotrichum. We sequenced and annotated the genomes of seven Mortierella isolates, and comparative predictions of KEGG orthologues using PICRUSt2 database updated with new genomes increased sequence reads coverage by 62.9% at the genus level. In addition, genes associated with carbohydrate and lipid metabolisms were differentially abundant between islands which remained undetected in the original database. Predicted functional pathways were similar across islands despite their geographical separation, difference in differentially abundant genes and composition. Our approach demonstrated the incorporation of the key taxa genomic data can improve functional gene prediction results and can be readily applied to investigate other niches of interests.

scholarly journals Extremely Halophilic Biohydrogen Producing Microbial Communities from High-Salinity Soil and Salt Evaporation Pond

Fuels ◽  
2021 ◽  
Vol 2 (2) ◽  
pp. 241-252
Author(s):  
Dyah Asri Handayani Taroepratjeka ◽  
Tsuyoshi Imai ◽  
Prapaipid Chairattanamanokorn ◽  
Alissara Reungsang
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
High Salinity ◽  
Amplicon Sequencing ◽  
Spatial Proximity ◽  
Lignocellulosic Waste ◽  
Evaporation Pond ◽  
Operational Taxonomic Units ◽  
Determining Factor

Extreme halophiles offer the advantage to save on the costs of sterilization and water for biohydrogen production from lignocellulosic waste after the pretreatment process with their ability to withstand extreme salt concentrations. This study identifies the dominant hydrogen-producing genera and species among the acclimatized, extremely halotolerant microbial communities taken from two salt-damaged soil locations in Khon Kaen and one location from the salt evaporation pond in Samut Sakhon, Thailand. The microbial communities’ V3–V4 regions of 16srRNA were analyzed using high-throughput amplicon sequencing. A total of 345 operational taxonomic units were obtained and the high-throughput sequencing confirmed that Firmicutes was the dominant phyla of the three communities. Halanaerobium fermentans and Halanaerobacter lacunarum were the dominant hydrogen-producing species of the communities. Spatial proximity was not found to be a determining factor for similarities between these extremely halophilic microbial communities. Through the study of the microbial communities, strategies can be developed to increase biohydrogen molar yield.

scholarly journals Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Sandra Reitmeier ◽  
Thomas C. A. Hitch ◽  
Nicole Treichel ◽  
Nikolaos Fikas ◽  
Bela Hausmann ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Diversity Analysis ◽  
Careful Attention ◽  
Operational Taxonomic Units ◽  
Basic Concepts ◽  
Gnotobiotic Mice ◽  
Mock Communities

Abstract16S rRNA gene amplicon sequencing is a popular approach for studying microbiomes. However, some basic concepts have still not been investigated comprehensively. We studied the occurrence of spurious sequences using defined microbial communities based on data either from the literature or generated in three sequencing facilities and analyzed via both operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) approaches. OTU clustering and singleton removal, a commonly used approach, delivered approximately 50% (mock communities) to 80% (gnotobiotic mice) spurious taxa. The fraction of spurious taxa was generally lower based on ASV analysis, but varied depending on the gene region targeted and the barcoding system used. A relative abundance of 0.25% was found as an effective threshold below which the analysis of spurious taxa can be prevented to a large extent in both OTU- and ASV-based analysis approaches. Using this cutoff improved the reproducibility of analysis, i.e., variation in richness estimates was reduced by 38% compared with singleton filtering using six human fecal samples across seven sequencing runs. Beta-diversity analysis of human fecal communities was markedly affected by both the filtering strategy and the type of phylogenetic distances used for comparison, highlighting the importance of carefully analyzing data before drawing conclusions on microbiome changes. In summary, handling of artifact sequences during bioinformatic processing of 16S rRNA gene amplicon data requires careful attention to avoid the generation of misleading findings. We propose the concept of effective richness to facilitate the comparison of alpha-diversity across studies.

scholarly journals From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data

GigaScience ◽  
2017 ◽  
Vol 6 (2) ◽  
Author(s):  
Mohamed Mysara ◽  
Mercy Njima ◽  
Natalie Leys ◽  
Jeroen Raes ◽  
Pieter Monsieurs
Keyword(s):  
Amplicon Sequencing ◽  
Sequencing Data ◽  
Operational Taxonomic Units ◽  
Processing Pipeline

scholarly journals Biogeography and Independent Diversification in the Protist Symbiont Community of Heterotermes tenuis

2021 ◽  
Vol 9 ◽  
Author(s):  
Francesca De Martini ◽  
Nicole L. Coots ◽  
Daniel E. Jasso-Selles ◽  
Jordyn Shevat ◽  
Alison Ravenscraft ◽  
...  
Keyword(s):  
Regional Differences ◽  
Amplicon Sequencing ◽  
Genetic Distances ◽  
Species Level ◽  
Mantel Tests ◽  
Geographical Distances ◽  
Host Phylogeny ◽  
Single Cell Isolation ◽  
Host Genetic ◽  
Protist Species

The eukaryotic microbiome of “lower” termites is highly stable and host-specific. This is due to the mutually obligate nature of the symbiosis and the direct inheritance of protists by proctodeal trophallaxis. However, vertical transmission is occasionally imperfect, resulting in daughter colonies that lack one or more of the expected protist species. This phenomenon could conceivably lead to regional differences in protist community composition within a host species. Here, we have characterized the protist symbiont community of Heterotermes tenuis (Hagen) (Blattodea: Rhinotermitidae) from samples spanning South and Central America. Using light microscopy, single cell isolation, and amplicon sequencing, we report eight species-level protist phylotypes belonging to four genera in the phylum Parabasalia. The diversity and distribution of each phylotype’s 18S rRNA amplicon sequence variants (ASVs) mostly did not correlate with geographical or host genetic distances according to Mantel tests, consistent with the lack of correlation we observed between host genetic and geographical distances. However, the ASV distances of Holomastigotoides Ht3 were significantly correlated with geography while those of Holomastigotoides Ht1 were significantly correlated with host phylogeny. These results suggest mechanisms by which termite-associated protist species may diversify independently of each other and of their hosts, shedding light on the coevolutionary dynamics of this important symbiosis.

scholarly journals Lactococcus lactis Diversity Revealed by Targeted Amplicon Sequencing of purR Gene, Metabolic Comparisons and Antimicrobial Properties in an Undefined Mixed Starter Culture Used for Soft-Cheese Manufacture

Foods ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 622
Author(s):  
Sabrina Saltaji ◽  
Olivier Rué ◽  
Valérie Sopena ◽  
Sophie Sablé ◽  
Fatoumata Tambadou ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Starter Culture ◽  
Antimicrobial Properties ◽  
Amplicon Sequencing ◽  
Antimicrobial Activities ◽  
Operational Taxonomic Units ◽  
Soft Cheese ◽  
Culture Independent ◽  
Identification Of Species ◽  
Species Specific

The undefined mixed starter culture (UMSC) is used in the manufacture of cheeses. Deciphering UMSC microbial diversity is important to optimize industrial processes. The UMSC was studied using culture-dependent and culture-independent based methods. MALDI-TOF MS enabled identification of species primarily from the Lactococcus genus. Comparisons of carbohydrate metabolism profiles allowed to discriminate five phenotypes of Lactococcus (n = 26/1616). The 16S sequences analysis (V1–V3, V3–V4 regions) clustered the UMSC microbial diversity into two Lactococcus operational taxonomic units (OTUs). These clustering results were improved with the DADA2 algorithm on the housekeeping purR sequences. Five L. lactis variants were detected among the UMSC. The whole-genome sequencing of six isolates allowed for the identification of the lactis subspecies using Illumina® (n = 5) and Pacbio® (n = 1) technologies. Kegg analysis confirmed the L. lactis species-specific niche adaptations and highlighted a progressive gene pseudogenization. Then, agar spot tests and agar well diffusion assays were used to assess UMSC antimicrobial activities. Of note, isolate supernatants (n = 34/1616) were shown to inhibit the growth of Salmonella ser. Typhimurium CIP 104115, Lactobacillus sakei CIP 104494, Staphylococcus aureus DSMZ 13661, Enterococcus faecalis CIP103015 and Listeria innocua CIP 80.11. Collectively, these results provide insightful information about UMSC L. lactis diversity and revealed a potential application as a bio-protective starter culture.

scholarly journals The Wheat Microbiome Under Four Management Strategies, and Potential for Endophytes in Disease Protection

2017 ◽  
Vol 1 (3) ◽  
pp. 158-168 ◽  
Author(s):  
Kristi Gdanetz ◽  
Frances Trail
Keyword(s):  
Bacterial Communities ◽  
Management Strategy ◽  
Crop Yields ◽  
Management Strategies ◽  
Growing Season ◽  
Amplicon Sequencing ◽  
Antagonistic Activity ◽  
Rrna Gene ◽  
Operational Taxonomic Units ◽  
Plant Organ

Manipulating plant-associated microbes to reduce disease or improve crop yields requires a thorough understanding of interactions within the phytobiome. Plants were sampled from a wheat/maize/soybean crop rotation site that implements four different crop management strategies. We analyzed the fungal and bacterial communities of leaves, stems, and roots of wheat throughout the growing season using 16S and fungal internal transcribed spacer 2 rRNA gene amplicon sequencing. The most prevalent operational taxonomic units (OTUs) were shared across all samples, although levels of the low-abundance OTUs varied. Endophytes were isolated from plants, and tested for antagonistic activity toward the wheat pathogen Fusarium graminearum. Antagonistic strains were assessed for plant protective activity in seedling assays. Our results suggest that microbial communities were strongly affected by plant organ and plant age, and may be influenced by management strategy.

scholarly journals The Effect of Coconut Oil Addition to Feed of Pigs on Rectal Microbial Diversity and Bacterial Abundance

Animals ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1764
Author(s):  
Michal Rolinec ◽  
Juraj Medo ◽  
Michal Gábor ◽  
Martina Miluchová ◽  
Daniel Bíro ◽  
...  
Keyword(s):  
Coconut Oil ◽  
Amplicon Sequencing ◽  
Normal Diet ◽  
Feeding Experiment ◽  
Bacterial Dna ◽  
Operational Taxonomic Units ◽  
Bacterial Groups ◽  
Sample Set ◽  
Positive Effect ◽  
Index Of Diversity

Coconut oil has a high content of lauric acid, which has selective antibacterial activity. This study aimed to explore the effect of coconut oil ingestion on the gastrointestinal microbiomes of pigs. A 14-day-long feeding experiment included 19 pigs in two groups (9 on a normal diet and 10 on a diet supplemented with coconut oil). At the start and end of the experiment, a rectal swab sample was taken from each pig in both groups, and total bacterial DNA was extracted. We used 16S rRNA high-throughput amplicon sequencing to evaluate the microbiome changes during the feeding experiment. A total of 446 operational taxonomic units (OTUs) were detected in the whole sample set. Shannon’s indices of bacterial diversity did not change significantly during the experiment. Changes in the bacterial community during the study period and in response to the coconut oil treatment were highly significant (p < 0.001). During the study, an increase in the abundance of Lactobacillus was detected in the group treated with coconut oil. An increase in Alloprevotella, Bifidobacteriales, and Lactobacillales and a decrease in Corynebacterium, Mitsuokella, Psychrobacter, and Pseudomonadales were attributed to the coconut oil treatment. Although the addition of coconut oil to pig feed did not affect Shannon’s index of diversity, it had a positive effect on the abundance of bacterial groups that are considered to be commensal and/or probiotic.

scholarly journals Inter-domain microbial diversity within the coral holobiontSiderastrea sidereafrom two depth habitats

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4323 ◽  
Author(s):  
Guido Bonthond ◽  
Daniel G. Merselis ◽  
Katherine E. Dougan ◽  
Trevor Graff ◽  
William Todd ◽  
...  
Keyword(s):  
Florida Keys ◽  
Amplicon Sequencing ◽  
Fungal Communities ◽  
Physiological Adaptation ◽  
Operational Taxonomic Units ◽  
Clade B ◽  
Holistic Understanding ◽  
Clade C ◽  
Occurrence Patterns ◽  
High Degree

Corals host diverse microbial communities that are involved in acclimatization, pathogen defense, and nutrient cycling. Surveys of coral-associated microbes have been particularly directed towardSymbiodiniumand bacteria. However, a holistic understanding of the total microbiome has been hindered by a lack of analyses bridging taxonomically disparate groups. Using high-throughput amplicon sequencing, we simultaneously characterized theSymbiodinium, bacterial, and fungal communities associated with the Caribbean coralSiderastrea sidereacollected from two depths (17 and 27 m) on Conch reef in the Florida Keys.S. sidereahosted an exceptionally diverseSymbiodiniumcommunity, structured differently between sampled depth habitats. While dominated at 27 m by aSymbiodiniumbelonging to clade C, at 17 mS. sidereaprimarily hosted a mixture of clade B types. Most fungal operational taxonomic units were distantly related to available reference sequences, indicating the presence of a high degree of fungal novelty within theS. sidereaholobiont and a lack of knowledge on the diversity of fungi on coral reefs. Network analysis showed that co-occurrence patterns in theS. sidereaholobiont were prevalent among bacteria, however, also detected between fungi and bacteria. Overall, our data show a drastic shift in the associatedSymbiodiniumcommunity between depths on Conch Reef, which might indicate that alteration in this community is an important mechanism facilitating local physiological adaptation of theS. sidereaholobiont. In contrast, bacterial and fungal communities were not structured differently between depth habitats.

scholarly journals Experimental evidence pointing to rain as a reservoir of tomato phyllosphere microbiota

2021 ◽  
Author(s):  
Marco Enrique Mechan Llontop ◽  
Long Tian ◽  
Parul Sharma ◽  
Logan Heflin ◽  
Vivian Angelica Bernal Galeano ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Microbial Population ◽  
Amplicon Sequencing ◽  
Crop Productivity ◽  
Sterile Water ◽  
Tomato Plants ◽  
Operational Taxonomic Units ◽  
16S Rrna Amplicon Sequencing ◽  
Plant Microbiota

Plant microbiota play essential roles in plant health and crop productivity. Comparisons of community composition have suggested seeds, soil, and the atmosphere as reservoirs of phyllosphere microbiota. After finding that leaves of tomato (Solanum lycopersicum) plants exposed to rain carried a higher microbial population size than leaves of tomato plants not exposed to rain, we experimentally tested the hypothesis that rain is a so far neglected reservoir of phyllosphere microbiota. Rain microbiota were thus compared with phyllosphere microbiota of tomato plants either treated with concentrated rain microbiota, filter-sterilized rain, or sterile water. Based on 16S rRNA amplicon sequencing, one-hundred and four operational taxonomic units (OTUs) significantly increased in relative abundance after inoculation with concentrated rain microbiota but no OTU significantly increased after treatment with either sterile water or filter-sterilized rain. Some of the genera to which these 104 OTUs belonged were also found at higher relative abundance on tomatoes exposed to rain outdoors than on tomatoes grown protected from rain in a commercial greenhouse. Taken together, these results point to precipitation as a reservoir of phyllosphere microbiota and show the potential of controlled experiments to investigate the role of different reservoirs in the assembly of phyllosphere microbiota.

scholarly journals Metataxonomic investigation of the microbial community in the trachea and oropharynx of healthy controls and diabetic patients using endotracheal tubes

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259596
Author(s):  
Sun Young Cho ◽  
Jeong-Hyun Choi ◽  
Seung Hyeun Lee ◽  
Yong-Sung Choi ◽  
Sung Wook Hwang ◽  
...  
Keyword(s):  
Endotracheal Tube ◽  
Amplicon Sequencing ◽  
Diabetic Patients ◽  
Healthy Controls ◽  
Additional Risk ◽  
Endotracheal Tubes ◽  
Operational Taxonomic Units ◽  
16S Amplicon Sequencing ◽  
Healthy Control ◽  
Respiratory Microbiota

Background Although the study of respiratory microbiota has been an active field of research, obtaining the appropriate respiratory samples for healthy controls remains to be a challenge. As such, this study aims to evaluate the use of endotracheal tube washing as a viable control for sputum samples. Methods A total of 14 subjects, including 8 healthy respiratory controls and 6 diabetic patients without any respiratory disease, were enrolled in this study, during which the endotracheal tubes used in their scheduled routine surgery were collected. Pre-operative oral gargles were also collected from non-diabetic subjects. Results 16S amplicon sequencing revealed similar taxa composition in endotracheal tube washings and oral gargles in the healthy control subjects, although the relative abundance of 11 genus level operational taxonomic units was significantly different between the two sample sources. The diabetic subjects showed relatively lower diversity than those of non-diabetic subjects. The proportion range of the most abundant taxa detected in each endotracheal tube washings were 10.1–33.2%. Conclusion Endotracheal tube washing fluid may provide healthy control samples for upper respiratory investigations without incurring any additional risk to the subject.

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