scholarly journals Deep microbial community profiling along the fermentation process of pulque, a major biocultural resource of Mexico

2019 ◽  
Author(s):  
Carolina Rocha-Arriaga ◽  
Annie Espinal-Centeno ◽  
Shamayim Martinez-Sanchez ◽  
Juan Caballero-Pérez ◽  
Luis D. Alcaraz ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Fermentation Process ◽  
Alcoholic Beverage ◽  
Essential Amino Acids ◽  
Fungal Species ◽  
Rrna Gene ◽  
List Type ◽  
Community Profiling ◽  
Massive Sequencing ◽  
Carl Von Linné

AbstractSome of the biggest non-three plants endemic to Mexico were called metl in the Nahua culture. During colonial times they were renamed with the antillan word maguey. This was changed again by Carl von Linné who called them Agave (a greco-latin voice for admirable). For several Mexican prehispanic cultures, Agave species were not only considered as crops, but also part of their biocultural resources and cosmovision. Among the major products obtained from some Agave spp since pre-hispanic times is the alcoholic beverage called pulque or octli. This beverage represents a precolumbian biotechnological development obtained by the natural fermentation of the mead (aguamiel) from such plants. The pulque played a central role in mexican prehispanic cultures, mainly the Mexica and the Tolteca, where it was considered as sacred. For modern Mexicans, pulque is still part of their heritage and, in recent times, there has been a renewed interest in this ancient beverage, due to its high content in nutrients such as essential amino acids. We focus this study in the microbial diversity involved in pulque fermentation process, specially because it is still produced using classic antique technologies,. In this work, we report the microbiome of pulque fermentation stages, using massive sequencing of the 16S rRNA gene and the internal transcribed spacer (ITS) for describing bacterial and fungal diversity and dynamics along pulque production. In this study, we are providing the most diverse catalogue of microbes during pulque production with 57 identified bacterial genus and 94 fungal species, these findings allowed us to identify core microbes resilient during pulque production which point to be potential biomarkers exclusive to each fermentation stage.Our approach allowed the identification of a broader microbial diversity in PulqueWe increased 4.4 times bacteria genera and 40 times fungal species detected in mead.Newly reported bacteria genera and fungal species associated to Pulque fermentation

scholarly journals Effects of Psychotropics on the Microbiome in Patients With Depression and Anxiety: Considerations in a Naturalistic Clinical Setting

2020 ◽  
Author(s):  
Yoshihiro Tomizawa ◽  
Shunya Kurokawa ◽  
Daiki Ishii ◽  
Katsuma Miyaho ◽  
Chiharu Ishii ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Diversity ◽  
Depressive Disorders ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Shannon Index ◽  
Rrna Gene ◽  
Depression And Anxiety ◽  
The Impact ◽  
Whole Tree

Abstract Background The antibacterial effects of psychotropics may be part of their pharmacological effects when treating depression. However, limited studies have focused on gut microbiota in relation to prescribed medication. Method We longitudinally investigated the relationship between patients’ prescribed medications and intestinal bacterial diversity in a naturalistic treatment course for patients with major depressive disorders and anxiety disorders. Patients were recruited and their stool was collected at 3 time points during their usual psychiatric treatments. Gut microbiota were analyzed using 16S rRNA gene sequencing. We examined the impact of psychotropics (i.e., antidepressants, anxiolytics, antipsychotics) on their gut microbial diversity and functions. Results We collected 246 stool samples from 40 patients. Despite no differences in microbial diversity between medication groups at the baseline, over the course of treatment, phylogenic diversity whole-tree diversity decreased in patients on antipsychotics compared with patients without (P = .027), and beta diversity followed this trend. Based on a fixed-effect model, antipsychotics predicted microbial diversity; the higher doses correlated with less diversity based on the Shannon index and phylogenic diversity whole tree (estimate = −0.00254, SE = 0.000595, P < .0001; estimate = −0.02644, SE = 0.00833, P = .002, respectively). Conclusion Antipsychotics may play a role in decreasing the alpha diversity of the gut microbiome among patients with depression and anxiety, and our results indicate a relationship with medication dosage. Future studies are warranted and should consider patients’ types and doses of antipsychotics in order to further elucidate the mechanisms of gut-brain interactions in psychiatric disorders.

scholarly journals Microbial Diversity of Terrestrial Geothermal Springs in Armenia and Nagorno-Karabakh: A Review

2021 ◽  
Vol 9 (7) ◽  
pp. 1473
Author(s):  
Ani Saghatelyan ◽  
Armine Margaryan ◽  
Hovik Panosyan ◽  
Nils-Kåre Birkeland
Keyword(s):  
16S Rrna ◽  
Microbial Diversity ◽  
High Altitude ◽  
Hot Springs ◽  
Hot Spring ◽  
Abiotic Factors ◽  
Rrna Gene ◽  
Geothermal Springs ◽  
Bacterial Phyla ◽  
Terrestrial Hot Springs

The microbial diversity of high-altitude geothermal springs has been recently assessed to explore their biotechnological potential. However, little is known regarding the microbiota of similar ecosystems located on the Armenian Highland. This review summarizes the known information on the microbiota of nine high-altitude mineralized geothermal springs (temperature range 25.8–70 °C and pH range 6.0–7.5) in Armenia and Nagorno-Karabakh. All these geothermal springs are at altitudes ranging from 960–2090 m above sea level and are located on the Alpide (Alpine–Himalayan) orogenic belt, a seismically active region. A mixed-cation mixed-anion composition, with total mineralization of 0.5 mg/L, has been identified for these thermal springs. The taxonomic diversity of hot spring microbiomes has been examined using culture-independent approaches, including denaturing gradient gel electrophoresis (DGGE), 16S rRNA gene library construction, 454 pyrosequencing, and Illumina HiSeq. The bacterial phyla Proteobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes are the predominant life forms in the studied springs. Archaea mainly include the phyla Euryarchaeota, Crenarchaeota, and Thaumarchaeota, and comprise less than 1% of the prokaryotic community. Comparison of microbial diversity in springs from Karvachar with that described for other terrestrial hot springs revealed that Proteobacteria, Bacteroidetes, Actinobacteria, and Deinococcus–Thermus are the common bacterial groups in terrestrial hot springs. Contemporaneously, specific bacterial and archaeal taxa were observed in different springs. Evaluation of the carbon, sulfur, and nitrogen metabolism in these hot spring communities has revealed diversity in terms of metabolic activity. Temperature seems to be an important factor in shaping the microbial communities of these springs. Overall, the diversity and richness of the microbiota are negatively affected by increasing temperature. Other abiotic factors, including pH, mineralization, and geological history, also impact the structure and function of the microbial community. More than 130 bacterial and archaeal strains (Bacillus, Geobacillus, Parageobacillus, Anoxybacillus, Paenibacillus, Brevibacillus Aeribacillus, Ureibacillus, Thermoactinomyces, Sporosarcina, Thermus, Rhodobacter, Thiospirillum, Thiocapsa, Rhodopseudomonas, Methylocaldum, Desulfomicrobium, Desulfovibrio, Treponema, Arcobacter, Nitropspira, and Methanoculleus) have been reported, some of which may be representative of novel species (sharing 91–97% sequence identity with their closest matches in GenBank) and producers of thermozymes and biomolecules with potential biotechnological applications. Whole-genome shotgun sequencing of T. scotoductus K1, as well as of the potentially new Treponema sp. J25 and Anoxybacillus sp. K1, were performed. Most of the phyla identified by 16S rRNA were also identified using metagenomic approaches. Detailed characterization of thermophilic isolates indicate the potential of the studied springs as a source of biotechnologically valuable microbes and biomolecules.

scholarly journals Microbial Diversity of Septic Tank Effluent and a Soil Biomat

2009 ◽  
Vol 75 (10) ◽  
pp. 3348-3351 ◽  
Author(s):  
Jill Tomaras ◽  
Jason W. Sahl ◽  
Robert L. Siegrist ◽  
John R. Spear
Keyword(s):  
Sequence Analysis ◽  
Microbial Diversity ◽  
Gene Sequence ◽  
Septic Tank ◽  
Rrna Gene ◽  
Control Soil ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Site Water ◽  
Septic Tank Effluent

ABSTRACT Microbial diversity of septic tank effluent (STE) and the biomat that is formed as a result of STE infiltration on soil were characterized by 16S rRNA gene sequence analysis. Results indicate that microbial communities are different within control soil, STE, and the biomat and that microbes found in STE are not found in the biomat. The development of a stable soil biomat appears to provide the best on-site water treatment or protection for subsequent groundwater interactions of STE.

scholarly journals Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5826 ◽  
Author(s):  
Muhammad Zarul Hanifah Md Zoqratt ◽  
Wilhelm Wei Han Eng ◽  
Binh Thanh Thai ◽  
Christopher M. Austin ◽  
Han Ming Gan
Keyword(s):  
16S Rrna ◽  
Microbial Diversity ◽  
Pond Water ◽  
Pacific White Shrimp ◽  
White Shrimp ◽  
Rrna Gene ◽  
Early Mortality Syndrome ◽  
The Pacific ◽  
High Sequence Conservation ◽  
Clustering Approach

Aquaculture production of the Pacific white shrimp is the largest in the world for crustacean species. Crucial to the sustainable global production of this important seafood species is a fundamental understanding of the shrimp gut microbiota and its relationship to the microbial ecology of shrimp pond. This is especially true, given the recently recognized role of beneficial microbes in promoting shrimp nutrient intake and in conferring resistance against pathogens. Unfortunately, aquaculture-related microbiome studies are scarce in Southeast Asia countries despite the severe impact of early mortality syndrome outbreaks on shrimp production in the region. In this study, we employed the 16S rRNA amplicon (V3–V4 region) sequencing and amplicon sequence variants (ASV) method to investigate the microbial diversity of shrimp guts and pond water samples collected from aquaculture farms located in Malaysia and Vietnam. Substantial differences in the pond microbiota were observed between countries with the presence and absence of several taxa extending to the family level. Microbial diversity of the shrimp gut was found to be generally lower than that of the pond environments with a few ubiquitous genera representing a majority of the shrimp gut microbial diversity such as Vibrio and Photobacterium, indicating host-specific selection of microbial species. Given the high sequence conservation of the 16S rRNA gene, we assessed its veracity at distinguishing Vibrio species based on nucleotide alignment against type strain reference sequences and demonstrated the utility of ASV approach in uncovering a wider diversity of Vibrio species compared to the conventional OTU clustering approach.

scholarly journals Microbial Diversity Analysis of Sediment from Nakdong River Estuary in the Republic of Korea Using 16S rRNA Gene Amplicon Sequencing

2018 ◽  
Vol 7 (14) ◽  
Author(s):  
Kyunghoi Kim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Diversity ◽  
Large Scale ◽  
Sediment Quality ◽  
River Estuary ◽  
Republic Of Korea ◽  
Rrna Gene ◽  
Nakdong River ◽  
The Republic

Deterioration of sediment quality has been found in the Nakdong River Estuary after large-scale reclamations. Here, I report microbial diversity in sediments of Nakdong River Estuary in the Republic of Korea based on 16S rRNA gene sequencing by next-generation sequencing (NGS) techniques.

scholarly journals OTUs clustering should be avoided for defining oral microbiome

2021 ◽  
Author(s):  
Alba Regueira-Iglesias ◽  
Lara Vazquez-Gonzalez ◽  
Carlos Balsa-Castro ◽  
Triana Blanco-Pintos ◽  
Victor Manuel Arce ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Operational Taxonomic Unit ◽  
Oral Bacteria ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
High Coverage ◽  
Archaeal Species ◽  
Health And Disease ◽  
Similarity Relationships

This in silico investigation aimed to: 1) evaluate a set of primer pairs with high coverage, including those most commonly used in the literature, to find the different oral species with 16S rRNA gene amplicon similarity/identity (ASI) values ≥97%; and 2) identify oral species that may be erroneously clustered in the same operational taxonomic unit (OTU) and ascertain whether they belong to distinct genera or other higher taxonomic ranks. Thirty-nine primer pairs were employed to obtain amplicon sequence variants (ASVs) from the complete genomes of 186 bacterial and 135 archaeal species. For each primer, ASVs without mismatches were aligned using BLASTN and their similarity values were obtained. Finally, we selected ASVs from different species with an ASI value ≥97% that were covered 100% by the query sequences. For each primer, the percentage of species-level coverage with no ASI≥97% (SC-NASI≥97%) was calculated. Based on the SC-NASI≥97% values, the best primer pairs were OP_F053-KP_R020 for bacteria (65.05%), KP_F018-KP_R002 for archaea (51.11%), and OP_F114-KP_R031 for bacteria and archaea together (52.02%). Eighty percent of the oral-bacteria and oral-archaea species shared an ASI≥97% with at least one other taxa, including Campylobacter, Rothia, Streptococcus, and Tannerella, which played conflicting roles in the oral microbiota. Moreover, around a quarter and a third of these two-by-two similarity relationships were between species from different bacteria and archaea genera, respectively. Furthermore, even taxa from distinct families, orders, and classes could be grouped in the same cluster. Consequently, irrespective of the primer pair used, OTUs constructed with a 97% similarity provide an inaccurate description of oral-bacterial and oral-archaeal species, greatly affecting microbial diversity parameters. As a result, clustering by OTUs impacts the credibility of the associations between some oral species and certain health and disease conditions. This limits significantly the comparability of the microbial diversity findings reported in oral microbiome literature.

scholarly journals Abundance and Microbial Diversity from Surface to Deep Water Layers Over the Rio Grande Rise, South Atlantic

2021 ◽  
Author(s):  
Juliana Correa Neiva Ferreira ◽  
Natascha M. Bergo ◽  
Pedro M. Tura ◽  
Mateus Gustavo Chuqui ◽  
Frederico P. Brandini ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Rio Grande ◽  
South Atlantic ◽  
Water Masses ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
List Type ◽  
Tropical Water ◽  
Southwestern Atlantic Ocean

AbstractMarine microbes control the flux of matter and energy essential for life in the oceans. Until now, the distribution and diversity of planktonic microorganisms above Fe-Mn crusts has received relatively little attention. Future mining\dredging of these minerals is predicted to affect microbial diversity and functioning in the deep sea. Here, we studied the ecology of planktonic microbes among pelagic environments of an Fe-Mn deposit region, at Rio Grande Rise, Southwestern Atlantic Ocean. We investigated microbial community composition using high-throughput sequencing of 16S rRNA genes and their abundance estimated by flow cytometry. Our results showed that the majority of picoplanktonic was found in epi- and mesopelagic waters, corresponding to the Tropical Water and South Atlantic Central Water. Bacterial and archaeal groups related to phototrophy, heterotrophy and chemosynthesis, such as Synechococcales, Sar11 (Proteobacteria) and Nitrosopumilales (Thaumarchaeota) were the main representatives of the pelagic microbial community. Additionally, we detected abundant assemblages involved in biodegradation of marine organic matter and iron oxidation at deep waters, i.e., Pseudoalteromonas and Alteromonas. No differences were observed in microbial community alpha diversity. However, we detected differences in community structure between water masses, suggesting that changes in an environmental setting (i.e. nutrient availability or circulation) play a significant role in structuring the pelagic zones, also affecting the meso- and bathypelagic microbiome.HighlightsRio Grande Rise pelagic microbiomePicoplankton carbon biomass partitioning through pelagic zonesUnique SAR11 Clade I oligotype in the shallowest Tropical WaterHigher number of shared oligotypes between deepest water massesNitrogen, carbon and sulfur may be important contributors for the pelagic microbiome

scholarly journals Microbial Diversity Profiling of Gut Microbiota of Macropus giganteus Using Three Hypervariable Regions of the Bacterial 16S rRNA

2021 ◽  
Vol 9 (8) ◽  
pp. 1721
Author(s):  
Christian O’Dea ◽  
Roger Huerlimann ◽  
Nicole Masters ◽  
Anna Kuballa ◽  
Cameron Veal ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Microbial Diversity ◽  
Surface Waters ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Faecal Contamination ◽  
Hypervariable Regions ◽  
Geographical Regions ◽  
V3 Region

Animal faecal contamination of surface waters poses a human health risk, as they may contain pathogenic bacteria or viruses. Of the numerous animal species residing along surface waterways in Australia, macropod species are a top contributor to wild animals’ faecal pollution load. We characterised the gut microbiota of 30 native Australian Eastern Grey Kangaroos from six geographical regions (five kangaroos from each region) within South East Queensland in order to establish their bacterial diversity and identify potential novel species-specific bacteria for the rapid detection of faecal contamination of surface waters by these animals. Using three hypervariable regions (HVRs) of the 16S rRNA gene (i.e., V1–V3, V3–V4, and V5–V6), for their effectiveness in delineating the gut microbial diversity, faecal samples from each region were pooled and microbial genomic DNA was extracted, sequenced, and analysed. Results indicated that V1-V3 yielded a higher taxa richness due to its larger target region (~480 bp); however, higher levels of unassigned taxa were observed using the V1-V3 region. In contrast, the V3–V4 HVR (~569 bp) attained a higher likelihood of a taxonomic hit identity to the bacterial species level, with a 5-fold decrease in unassigned taxa. There were distinct dissimilarities in beta diversity between the regions, with the V1-V3 region displaying the highest number of unique taxa (n = 42), followed by V3–V4 (n = 11) and V5–V6 (n = 8). Variations in the gut microbial diversity profiles of kangaroos from different regions were also observed, which indicates that environmental factors may impact the microbial development and, thus, the composition of the gut microbiome of these animals.

scholarly journals How, when, and where relic DNA biases estimates of microbial diversity

2017 ◽  
Author(s):  
JT Lennon ◽  
ME Muscarella ◽  
SA Muscarella ◽  
BK Lehmkuhl
Keyword(s):  
Microbial Diversity ◽  
Dna Sequences ◽  
Species Abundance ◽  
Rrna Gene ◽  
Bacterial Dna ◽  
Soil Sediment ◽  
Species Abundance Distributions ◽  
Abundance And Diversity ◽  
Dna Pool ◽  
Biased Estimates

Extracellular or “relic” DNA is one of the largest pools of nucleic acids in the mbiosphere1,2. Relic DNA can influence a number of important ecological and evolutionary processes, but it may also bias estimates of microbial abundance and diversity, which has implications for understanding environmental, engineered, and host-associated ecosystems. We developed models capturing the fundamental processes that regulate the size and composition of the relic DNA pools to identify scenarios leading to biased estimates of biodiversity. Our models predict that bias increases with relic DNA pool size, but only when the species abundance distributions (SAD) of relic and intact DNA are distinct from one another. We evaluated our model predictions by quantifying relic DNA and assessing its contribution to bacterial diversity using 16S rRNA gene sequences collected from different ecosystem types, including soil, sediment, water, and the mammalian gut. On average, relic DNA made up 33 % of the total bacterial DNA pool, but exceeded 80 % in some samples. Despite its abundance, relic DNA had no effect on estimates of taxonomic and phylogenetic diversity, even in ecosystems where processes such as the physical protection of relic DNA are common and predicted by our models to generate bias. Rather, our findings are consistent with the expectation that relic DNA sequences degrade in proportion to their abundance and therefore may contribute minimally to estimates of microbial diversity.

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