The cultivation of Pyropia haitanensis has important impacts on the seawater microbial community

Abstract Microorganisms play important roles in the growth and development of macroalgae. Still, the biodiversity of the epiphytic microbial community associated with the economically important red alga Pyropia haitanensis during the cultivation period remains uncharacterized, especially the effects of P. haitanensis cultivation on the microbial community of surrounding seawater. Here, we isolated epiphytic microbes from P. haitanensis during the thallus stage during oceanic cultivation and the conchocelis stage during industrial cultivation. The dynamic diversity patterns, as determined by 16S and 18S rRNA gene sequencing of the bacterial and fungal communities, respectively, associated with P. haitanensis and seawater in the presence and absence of algal cultivation were investigated. A notable distinction was observed between the microbial communities of seawater with and without P. haitanensis cultivation. Additionally, the alpha-diversity of seawater with P. haitanensis cultivation was significantly greater than without P. haitanensis cultivation. Cyanobacteria were the dominant species in the latter, while Rhodobacteraceae was enriched in the former. Furthermore, there were significant differences in the microbial community of P. haitanensis at the thallus and conchocelis stages. Seawater properties had significant direct effects on the microbial diversity of P. haitanensis and cultivation seawater, but not on non-cultivation seawater. The enriched microbial presence might promote thallus morphogenesis and be beneficial for the growth and development of both the thallus and conchocelis stages. These findings expand our knowledge of the bacteria and fungi that are beneficial for Pyropia nursery seeding and cultivation, as well as the effects of P. haitanensis cultivation on the seawater microbial community.

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Responses of microbial community from tropical pristine coastal soil to crude oil contamination

10.7287/peerj.preprints.1254v1 ◽

2015 ◽

Author(s):

Daniel Morais ◽

Victor Pylro ◽

Ian M Clark ◽

Penny R Hirsch ◽

Marcos Tótola

Keyword(s):

Microbial Community ◽

Crude Oil ◽

Alpha Diversity ◽

Illumina Miseq ◽

Oil Reservoirs ◽

Rrna Gene ◽

Community Shift ◽

Campos Basin ◽

Trindade Island ◽

Bacteria And Fungi

Crude oil is still the dominant energy source in Brazil and that the consumption keeps rising since 2013, being responsible for 2.2% of the world’s energy consumption. The recent discovery of crude oil reservoirs at the Espirito Santo basin, Campos basin and Santos basin, can be considered as an excellent opportunity to supply the country’s economic and energetic demands. However, albeit the opportunity these crude oil reservoirs represent, offshore exploration offers risks to the microbiota and the whole sea life, as petroleum hydrocarbons are toxic, mutagenic, teratogenic and carcinogenic. Microbes are responsible for nutrient cycling and can degrade even very recalcitrant hydrocarbons. This work aimed to evaluate the microbial community shift (Archaea, Bacteria and Fungi) from Trindade Island coastal environment under petroleum contamination. Microcosms were assembled using Trindade Island coastal soil to create two treatments, control and contaminated (weathered crude oil at 30 g kg-1). Soils were incubated during 38 days with CO2 measurements every four hours. Total DNA was extracted, purified and submited for sequencing of 16s rRNA gene, for Bacteria and Archaea domains and Fungal ITS1 region using Illumina MiSeq platform. We compared alpha diversity, beta diversity and taxonomic shifts between controls and contaminated samples. Three days after contamination, emission rate peaked at more than 20x the control and the emissions remained higer during the whole incubation period. Microbial alpha diversity was reduced for contaminated-samples. Fungi community of contaminated samples was reduced to almost 40% of the observed species. Taxonomy comparisons showed rise of the Actinobacteria phylum and reduction of the Archaea Candidatus nitrosphaere.

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Modulation of Saliva Microbiota through Prebiotic Intervention in HIV-Infected Individuals

Nutrients ◽

10.3390/nu11061346 ◽

2019 ◽

Vol 11 (6) ◽

pp. 1346 ◽

Cited By ~ 1

Author(s):

Nuria Jiménez-Hernández ◽

Sergio Serrano-Villar ◽

Alba Domingo ◽

Xavier Pons ◽

Alejandro Artacho ◽

...

Keyword(s):

Hiv Infection ◽

Alpha Diversity ◽

Rrna Gene ◽

Oral Microbiota ◽

Microbiota Composition ◽

Hiv Status ◽

T Helper ◽

Immunodeficiency Virus ◽

Salivary Microbiota ◽

Rrna Gene Sequencing

Human immunodeficiency virus (HIV) infection is characterized by an early depletion of the mucosal associated T helper (CD4+) cells that impair the host immunity and impact the oral and gut microbiomes. Although, the HIV-associated gut microbiota was studied in depth, few works addressed the dysbiosis of oral microbiota in HIV infection and, to our knowledge, no studies on intervention with prebiotics were performed. We studied the effect of a six-week-long prebiotic administration on the salivary microbiota in HIV patients and healthy subjects. Also, the co-occurrence of saliva microorganisms in the fecal bacteria community was explored. We assessed salivary and feces microbiota composition using deep 16S ribosomal RNA (rRNA) gene sequencing with Illumina methodology. At baseline, the different groups shared the same most abundant genera, but the HIV status had an impact on the saliva microbiota composition and diversity parameters. After the intervention with prebiotics, we found a drastic decrease in alpha diversity parameters, as well as a change of beta diversity, without a clear directionality toward a healthy microbiota. Interestingly, we found a differential response to the prebiotics, depending on the initial microbiota. On the basis of 100% identity clustering, we detected saliva sequences in the feces datasets, suggesting a drag of microorganisms from the upper to the lower gastrointestinal tract.

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Nutrient dynamics and stream order influence microbial community patterns along a 2914 km transect of the Mississippi River

10.1101/091512 ◽

2016 ◽

Cited By ~ 1

Author(s):

Michael W. Henson ◽

Jordan Hanssen ◽

Greg Spooner ◽

Patrick Fleming ◽

Markus Pukonen ◽

...

Keyword(s):

Water Quality ◽

Microbial Community ◽

Mississippi River ◽

Nutrient Dynamics ◽

18S Rrna Gene ◽

Rrna Gene ◽

Ohio River ◽

Core Microbiome ◽

Water Transportation ◽

River Confluence

AbstractDraining 31 states and roughly 3 million km2, the Mississippi River (MSR) and its tributaries constitute an essential resource to millions of people for clean drinking water, transportation, agriculture, and industry. Since the turn of the 20thcentury, MSR water quality has continually rated poorly due to human activity. Acting as first responders, microorganisms can mitigate, exacerbate, and/or serve as predictors for water quality, yet we know little about their community structure or ecology at the whole river scale for large rivers. We collected both biological (16S and 18S rRNA gene amplicons) and physicochemical data from 38 MSR sites over nearly 3000 km from Minnesota to the Gulf of Mexico. Our results revealed a microbial community composed of similar taxa to other rivers but with unique trends in the relative abundance patterns among phyla, OTUs, and the core microbiome. Furthermore, we observed a separation in microbial communities that mirrored the transition from an 8thto 10thStrahler order river at the Missouri River confluence, marking a different start to the lower MSR than the historical distinction at the Ohio River confluence in Cairo, IL. Within MSR microbial assemblages we identified subgroups of OTUs from the phyla Acidobacteria, Bacteroidetes, Oomycetes, and Heterokonts that were associated with, and predictive of, the important eutrophication nutrients nitrate and phosphate. This study offers the most comprehensive view of MSR microbiota to date, provides important groundwork for higher resolution microbial studies of river perturbation, and identifies potential microbial indicators of river health related to eutrophication.

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Long-chain diols in rivers: distribution and potential biological sources

10.5194/bg-2018-116 ◽

2018 ◽

Cited By ~ 1

Author(s):

Julie Lattaud ◽

Frédérique Kirkels ◽

Francien Peterse ◽

Chantal V. Freymond ◽

Timothy I. Eglinton ◽

...

Keyword(s):

River Flow ◽

18S Rrna Gene ◽

Rrna Gene ◽

River Systems ◽

Eukaryotic Diversity ◽

Suspended Particulate ◽

Fractional Abundance ◽

Biological Sources ◽

Rrna Gene Sequencing ◽

Long Chain

Abstract. Long chain diols (LCDs) occur widespread in marine environments and also in lakes and rivers. Transport of LCDs from rivers may impact the distribution of LCDs in coastal environments, however relatively little is known about the distribution and biological sources of LCDs in river systems. In this study, we investigated the distribution of LCDs in suspended particulate matter (SPM) of three river systems (Godavari, Danube, and Rhine) in relation with season, precipitation, temperature, and source catchments. The dominant long-chain diol is the C32 1,15-diol followed by the C30 1,15-diol in all studied river systems. In regions influenced by marine waters, such as delta systems, the fractional abundance of the C30 1,15-diol is substantially higher than in the river itself, suggesting different LCD producers in marine and freshwater environments. A change in the LCD distribution along the downstream transects of the rivers studied was not observed. However, an effect of river flow is observed, i.e. the concentration of the C32 1,15-diol is higher in stagnant waters, such as reservoirs and during seasons with river low stands. A seasonal change in the LCD distribution was observed in the Rhine, likely due to a change in the producers. Eukaryotic diversity analysis by 18S rRNA gene sequencing of SPM from the Rhine showed extremely low abundances of sequences (i.e.

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Arsenic mobilization in a high arsenic groundwater revealed by metagenomic and Geochip analyses

Scientific Reports ◽

10.1038/s41598-019-49365-w ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Zhou Jiang ◽

Ping Li ◽

Yanhong Wang ◽

Han Liu ◽

Dazhun Wei ◽

...

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Arsenic Mobilization ◽

Rrna Gene Sequencing ◽

High Arsenic ◽

High Arsenic Groundwater

Abstract Microbial metabolisms of arsenic, iron, sulfur, nitrogen and organic matter play important roles in arsenic mobilization in aquifer. In this study, microbial community composition and functional potentials in a high arsenic groundwater were investigated using integrated techniques of RNA- and DNA-based 16S rRNA gene sequencing, metagenomic sequencing and functional gene arrays. 16S rRNA gene sequencing showed the sample was dominated by members of Proteobacteria (62.3–75.2%), such as genera of Simplicispira (5.7–6.7%), Pseudomonas (3.3–5.7%), Ferribacterium (1.6–4.4%), Solimonas (1.8–3.2%), Geobacter (0.8–2.2%) and Sediminibacterium (0.6–2.4%). Functional potential analyses indicated that organics degradation, assimilatory sulfate reduction, As-resistant pathway, iron reduction, ammonification, nitrogen fixation, denitrification and dissimilatory nitrate reduction to ammonia were prevalent. The composition and function of microbial community and reconstructed genome bins suggest that high level of arsenite in the groundwater may be attributed to arsenate release from iron oxides reductive dissolution by the iron-reducing bacteria, and subsequent arsenate reduction by ammonia-producing bacteria featuring ars operon. This study highlights the relationship between biogeochemical cycling of arsenic and nitrogen in groundwater, which potentially occur in other aquifers with high levels of ammonia and arsenic.

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Influences of Ingredients and Bakers on the Bacteria and Fungi in Sourdough Starters and Bread

mSphere ◽

10.1128/msphere.00950-19 ◽

2020 ◽

Vol 5 (1) ◽

Cited By ~ 4

Author(s):

Aspen T. Reese ◽

Anne A. Madden ◽

Marie Joossens ◽

Guylaine Lacaze ◽

Robert R. Dunn

Keyword(s):

Microbial Community ◽

Internal Transcribed Spacer ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Skin Microbiome ◽

Relative Importance ◽

Naturally Occurring ◽

Sourdough Bread ◽

Bacteria And Fungi ◽

Bidirectional Exchange

ABSTRACT Sourdough starters are naturally occurring microbial communities in which the environment, ingredients, and bakers are potential sources of microorganisms. The relative importance of these pools remains unknown. Here, bakers from two continents used a standardized recipe and ingredients to make starters that were then baked into breads. We characterized the fungi and bacteria associated with the starters, bakers’ hands, and ingredients using 16S and internal transcribed spacer (ITS) rRNA gene amplicon sequencing and then measured dough acidity and bread flavor. Starter communities were much less uniform than expected, and this variation manifested in the flavor of the bread. Starter communities were most similar to those found in flour but shared some species with the bakers’ skin. While humans likely contribute microorganisms to the starters, the reverse also appears to be true. This bidirectional exchange of microorganisms between starters and bakers highlights the importance of microbial diversity on bodies and in our environments as it relates to foods. IMPORTANCE Sourdough starters are complex communities of yeast and bacteria which confer characteristic flavor and texture to sourdough bread. The microbes present in starters can be sourced from ingredients or the baking environment and are typically consistent over time. Herein, we show that even when the recipe and ingredients for starter and bread are identical, different bakers around the globe produce highly diverse starters which then alter bread acidity and flavor. Much of the starter microbial community comes from bread flour, but the diversity is also associated with differences in the microbial community on the hands of bakers. These results indicate that bakers may be a source for yeast and bacteria in their breads and/or that bakers’ jobs are reflected in their skin microbiome.

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Age-Related Colonic Mucosal Microbiome Community Shifts in Monkeys

The Journals of Gerontology Series A ◽

10.1093/gerona/glaa256 ◽

2020 ◽

Author(s):

Ravichandra Vemuri ◽

Chrissy Sherrill ◽

Matthew A Davis ◽

Kylie Kavanagh

Keyword(s):

Microbial Community ◽

Systemic Inflammation ◽

16S Rrna Gene Sequencing ◽

Microbial Interactions ◽

Rrna Gene ◽

Vervet Monkeys ◽

Fecal Samples ◽

Age Related ◽

Rrna Gene Sequencing ◽

The Stability

Abstract Age-related changes in gut microbiome impact host health. The interactive relationship between the microbiome and physiological systems in an aged body system remains to be clearly defined, particularly in the context of inflammation. Therefore, we aimed to evaluate systemic inflammation, microbial translocation (MT), and differences between fecal and mucosal microbiomes. Ascending colon mucosal biopsies, fecal samples, and blood samples from healthy young and old female vervet monkeys were collected for 16S rRNA gene sequencing, MT, and cytokine analyses, respectively. To demonstrate microbial co-occurrence patterns, we used Kendall’s tau correlation measure of interactions between microbes. We found elevated levels of plasma LBP-1, MCP-1, and CRP in old monkeys, indicative of higher MT and systemic inflammation. Microbiome analysis revealed significant differences specific to age. At the phylum level, abundances of pathobionts such as Proteobacteria were increased in the mucosa of old monkeys. At the family level, Helicobacteriaceae was highly abundant in mucosal samples (old); in contrast, Ruminococcaceae were higher in the fecal samples of old monkeys. We found significantly lower Firmicutes:Bacteroidetes ratio and lower abundance of butyrate-producing microbes in old monkeys, consistent with less healthy profiles. Microbial community co-occurrence analysis on mucosal samples revealed 13 nodes and 41 associations in the young monkeys, but only 12 nodes and 21 associations in the old monkeys. Our findings provide novel insights into systemic inflammation and gut microbial interactions, highlight the importance of the mucosal niche, and facilitate further understanding of the decline in the stability of the microbial community with aging.

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Metataxonomics contributes to unravel the microbiota of a Brazilian dairy

Journal of Dairy Research ◽

10.1017/s0022029920000837 ◽

2020 ◽

Vol 87 (3) ◽

pp. 360-363

Author(s):

Diego Araújo Frazilio ◽

Otávio Guilherme Gonçalves de Almeida ◽

Carlos Augusto Fernandes de Oliveira ◽

Sarah Hwa In Lee ◽

Carlos Humberto Corassin ◽

...

Keyword(s):

Alpha Diversity ◽

16S Rrna Gene Sequencing ◽

Raw Material ◽

Rrna Gene ◽

Food Protection ◽

The Core ◽

Food Contact ◽

Food Contact Surfaces ◽

Contact Surfaces ◽

Rrna Gene Sequencing

AbstractFor this research communication, 90 samples of a Brazilian dairy were combined into four groups (raw material, final product, food-contact and non-food contact surfaces) and analyzed by metataxonomics based on 16S rRNA gene sequencing. The results showed high alpha-diversity indexes for final product and non-food contact surfaces but, overall, beta-diversity indexes were low. The samples were separated in two main clusters, and the core microbiota was composed by Macrococcus, Alkaliphilus, Vagococcus, Lactobacillus, Marinilactibacillus, Streptococcus, Lysinibacillus, Staphylococcus, Clostridium, Halomonas, Lactococcus, Enterococcus, Bacillus and Psychrobacter. These results highlight that rare taxa occur in dairies, and this may aid the development of strategies for food protection.

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Stenamoeba dejonckheerei sp. nov., a Free-Living Amoeba Isolated from a Thermal Spring

Pathogens ◽

10.3390/pathogens9070586 ◽

2020 ◽

Vol 9 (7) ◽

pp. 586

Author(s):

Manuel Alejandro Borquez-Román ◽

Luis Fernando Lares-Jiménez ◽

Libia Zulema Rodriguez-Anaya ◽

Jose Reyes Gonzalez-Galaviz ◽

Paul A. Fuerst ◽

...

Keyword(s):

Thermal Spring ◽

Small Subunit ◽

18S Rrna Gene ◽

Rrna Gene ◽

Likelihood Analysis ◽

Ribosomal Ribonucleic Acid ◽

Pcr Products ◽

Northwestern Mexico ◽

Rrna Gene Sequencing ◽

A New Species

Two amoeboid organisms were obtained from water samples taken from a thermal spring, "Agua Caliente", in Northwestern Mexico. The isolates were obtained when samples were cultivated at 37 °C on non-nutrient agar coated with Escherichia coli. The initial identification of the isolates was performed morphologically using light microscopy. The samples were found to have trophozoite morphology consistent with members of the genus Stenamoeba, a genus derived in 2007 from within the abolished polyphyletic genus Platyamoeba. Further analysis was performed by sequencing PCR products obtained using universal eukaryotic primers for the small subunit ribosomal ribonucleic acid (SSU rRNA) gene. Sequencing primers were designed to allow the comparison of the 18S rRNA gene sequences of the new isolates with previous sequences reported for Stenamoeba. Phylogenetic relationships among sequences from Stenamoeba were determined using Maximum Likelihood analysis. The results showed the two "Agua Caliente" sequences to be closely related, while clearly separating them from those of other Stenamoeba taxa. The degrees of sequence differentiation from other taxa were considered sufficient to allow us to propose that the Mexican isolates represent a new species.

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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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