scholarly journals Station and train surface microbiomes of Mexico City’s metro (subway/underground)

2019 ◽  
Author(s):  
Apolinar Misael Hernández ◽  
Daniela Vargas-Robles ◽  
Luis D. Alcaraz ◽  
Mariana Peimbert
Keyword(s):  
Mexico City ◽  
Urban Systems ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Normal Human Skin ◽  
Massive Sequencing ◽  
Normal Human ◽  
Diversity Profile ◽  
The 16S Rrna Gene ◽  
Environmental Microbes

AbstractThe metro is one of the more representative urban systems of Mexico City, and it transports approximately 4.5 million commuters every day. Large crowds promote the constant exchange of human and environmental microbes. In this study, we determined the bacterial diversity profile of the Mexico City subway by massive sequencing of the 16S rRNA gene. We identified a total of 50,197 operative taxonomic units (OTUs) and 1058 genera. The metro microbiome was dominated by the phylum Actinobacteria and by the genera Propionibacterium (15%) (P. acnes 13%), Corynebacterium (13%), Streptococcus (9%), and Staphylococcus (5%) (S. epidermidis; 4%), reflecting the microbe composition of normal human skin. The metro microbial sources were skin, dust, saliva, and vaginal, with no fecal contribution detected. A total of 420 bacterial genera were universal to the twelve metro lines tested, and they contributed to 99.10% of the abundance. The large OTUs number are probably reflecting the vast human influx, while selection from hosts and environments are constraining the genera diversity, shown by the OTUs to genus ratio. Finally, this study shows that the microbial composition of the Mexico City subway comes from a mixture of environmental and human sources and that commuters are exposed to normal human microbiota.

scholarly journals Host reproductive cycle influences the pouch microbiota of wild southern hairy-nosed wombats (Lasiorhinus latifrons)

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Sesilje Weiss ◽  
David Taggart ◽  
Ian Smith ◽  
Kristofer M. Helgen ◽  
Raphael Eisenhofer
Keyword(s):  
Microbial Community ◽  
Reproductive Cycle ◽  
Tammar Wallaby ◽  
The Body ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Birth Canal ◽  
Gram Positive Bacteria ◽  
Rigorous Framework ◽  
The 16S Rrna Gene

Abstract Background Marsupials are born much earlier than placental mammals, with most crawling from the birth canal to the protective marsupium (pouch) to further their development. However, little is known about the microbiology of the pouch and how it changes throughout a marsupial’s reproductive cycle. Here, using stringent controls, we characterized the microbial composition of multiple body sites from 26 wild Southern Hairy-nosed Wombats (SHNWs), including pouch samples from animals at different reproductive stages. Results Using qPCR of the 16S rRNA gene we detected a microbial community in the SHNW pouch. We observed significant differences in microbial composition and diversity between the body sites tested, as well as between pouch samples from different reproductive stages. The pouches of reproductively active females had drastically lower microbial diversity (mean ASV richness 19 ± 8) compared to reproductively inactive females (mean ASV richness 941 ± 393) and were dominated by gram positive bacteria from the Actinobacteriota phylum (81.7–90.6%), with the dominant families classified as Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, and Dietziaceae. Three of the five most abundant sequences identified in reproductively active pouches had closest matches to microbes previously isolated from tammar wallaby pouches. Conclusions This study represents the first contamination-controlled investigation into the marsupial pouch microbiota, and sets a rigorous framework for future pouch microbiota studies. Our results indicate that SHNW pouches contain communities of microorganisms that are substantially altered by the host reproductive cycle. We recommend further investigation into the roles that pouch microorganisms may play in marsupial reproductive health and joey survival.

scholarly journals The Microbial Communities of Leaves and Roots Associated with Turtle Grass (Thalassia testudinum) and Manatee Grass (Syringodium filliforme) are Distinct from Seawater and Sediment Communities, but Are Similar between Species and Sampling Sites

2018 ◽  
Vol 7 (1) ◽  
pp. 4 ◽  
Author(s):  
Kelly Ugarelli ◽  
Peeter Laas ◽  
Ulrich Stingl
Keyword(s):  
Carbon Sink ◽  
Amplicon Sequencing ◽  
Thalassia Testudinum ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Carbon Cycles ◽  
Syringodium Filiforme ◽  
Turtle Grass ◽  
Shoreline Protection ◽  
The 16S Rrna Gene

Seagrasses are vital members of coastal systems, which provide several important ecosystem services such as improvement of water quality, shoreline protection, and serving as shelter, food, and nursery to many species, including economically important fish. They also act as a major carbon sink and supply copious amounts of oxygen to the ocean. A decline in seagrasses has been observed worldwide, partly due to climate change, direct and indirect human activities, diseases, and increased sulfide concentrations in the coastal porewaters. Several studies have shown a symbiotic relationship between seagrasses and their microbiome. For instance, the sulfur, nitrogen, and carbon cycles are important biochemical pathways that seem to be linked between the plant and its microbiome. The microbiome presumably also plays a key role in the health of the plant, for example in oxidizing phyto-toxic sulfide into non-toxic sulfate, or by providing protection for seagrasses from pathogens. Two of the most abundant seagrasses in Florida include Thalassia testudinum (turtle grass) and Syringodium filliforme (manatee grass), yet there is little data on the composition of the microbiome of these two genera. In this study, the microbial composition of the phyllosphere and rhizosphere of Thalassia testudinum and Syringodium filiforme were compared to water and sediment controls using amplicon sequencing of the V4 region of the 16S rRNA gene. The microbial composition of the leaves, roots, seawater, and sediment differ from one another, but are similar between the two species of seagrasses.

scholarly journals Faecal bacterial composition in dairy cows shedding Mycobacterium avium subsp. paratuberculosis in faeces in comparison with nonshedding cows

2016 ◽  
Vol 62 (6) ◽  
pp. 538-541 ◽  
Author(s):  
Marija Kaevska ◽  
Petra Videnska ◽  
Karel Sedlar ◽  
Iva Bartejsova ◽  
Alena Kralova ◽  
...  
Keyword(s):  
Dairy Cows ◽  
Mycobacterium Avium ◽  
Mycobacterium Avium Subsp ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Bacterial Composition ◽  
Bacterial Populations ◽  
Faecal Samples ◽  
Mycobacterium Avium Subsp Paratuberculosis ◽  
The 16S Rrna Gene

The aim of this study was to determine possible differences in the faecal microbiota of dairy cows infected with Mycobacterium avium subsp. paratuberculosis (Johne’s disease) in comparison with noninfected cows from the same herds. Faecal samples from cows in 4 herds were tested for M. avium subsp. paratuberculosis by real-time PCR, and faecal bacterial populations were analysed by 454 pyrosequencing of the 16S rRNA gene. The most notable differences between shedding and nonshedding cows were an increase in the genus Psychrobacter and a decrease in the genera Oscillospira, Ruminococcus, and Bifidobacterium in cows infected with M. avium subsp. paratuberculosis. The present study is the first to report the faecal microbial composition in dairy cows infected with M. avium subsp. paratuberculosis.

scholarly journals Host reproductive cycle influences the pouch microbiota of wild Southern Hairy-nosed Wombats (Lasiorhinus latifrons)

2021 ◽  
Author(s):  
Sesilje Weiss ◽  
David Taggart ◽  
Ian Smith ◽  
Kristofer M Helgen ◽  
Raphael Eisenhofer
Keyword(s):  
Microbial Community ◽  
Reproductive Cycle ◽  
Tammar Wallaby ◽  
The Body ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Birth Canal ◽  
Gram Positive Bacteria ◽  
Rigorous Framework ◽  
The 16S Rrna Gene

Abstract Background Marsupials are born much earlier than placental mammals, with most crawling from the birth canal to the protective marsupium (pouch) to further their development. However, little is known about the microbiology of the pouch and how it changes throughout a marsupial’s reproductive cycle. Here, using stringent controls, we characterized the microbial composition of multiple body sites from 26 wild Southern Hairy-nosed Wombats (SHNWs), including pouch samples from animals at different reproductive stages. Results Using qPCR of the 16S rRNA gene we detected a microbial community in the SHNW pouch. We observed significant differences in microbial composition and diversity between the body sites tested, as well as between pouch samples from different reproductive stages. The pouches of reproductively active females had drastically lower microbial diversity (mean ASV richness 19 ± 8) compared to reproductively inactive females (mean ASV richness 941 ± 393) and were dominated by gram positive bacteria from the Actinobacteriota phylum (81.7-90.6%), with the dominant families classified as Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, and Dietziaceae. Three of the five most abundant sequences identified in reproductively active pouches had closest matches to microbes previously isolated from tammar wallaby pouches. Conclusions This study represents the first contamination-controlled investigation into the marsupial pouch microbiota, and sets a rigorous framework for future pouch microbiota studies. Our results indicate that SHNW pouches contain communities of microorganisms that are substantially altered by the host reproductive cycle. We recommend further investigation into the roles that pouch microorganisms may play in marsupial reproductive health and joey survival.

scholarly journals Alkalo-Thermophilic Microbial Diversity of the Tecozautla Geyser, México

2021 ◽  
Author(s):  
Jesus Alberto Segovia-Cruz ◽  
Valeria Souza ◽  
Yuridia Mercado-Flores ◽  
Miguel Angel Anducho-Reyes ◽  
Genaro Vargas-Hernández ◽  
...  
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
Software Package ◽  
Microbial Mats ◽  
Rrna Gene ◽  
Thermal Systems ◽  
Microbial Composition ◽  
Salt Deposits ◽  
The 16S Rrna Gene ◽  
Storage Pools

Abstract Microbial mats have been studied in many thermal systems; the most iconic is Yellowstone. In Mexico, the information on microbial mats is scarce and therefore novel. In this research, the thermophilic microbial composition of samples from four areas of the Tecozautla geyser, Hidalgo, Mexico, was studied: sediments (GD), salt deposits (GA), and microbial mats (GB and GC). The samples were taken at the outlet of the geyser (94 °C) and in storage pools with temperatures of 61.5-65 °C. Sequencing of the 16S rRNA gene amplicons was carried out, obtaining 1,425,506 readings, and was analyzed through the Quantitative Insights Into Microbial Ecology software package version 2 (qiime2). 32 phyla were identified in the four samples being the most representative for the GA sample: Armatimonadetes, Chloroflexi, Cyanobacteria, and Thermi, with abundances of 46.35, 19.18, 3.27, and 1.82 %, respectively. For the GB sample, they were Proteobacteria, Bacteroidetes, Cyanobacteria, Spirochaetes, Thermi, and Firmicutes with abundances of 25.23, 22.04, 20.42, 12.31, 4.56, and 1.32 %, respectively. For the GC sample, abundances of 55.60, 9.85, 7.04, 7.01, and 6.15 % were observed for the phylum Chloroflexi, Armatimonadetes, Proteobacteria, Cyanobacteria, and Acidobacteria, respectively. Finally, for the GD sample, the most abundant phyla were Chloroflexi (36.10 %), Cyanobacteria (17.13 %), Armatimonadetes (15.59 %), Proteobacteria (5.45 %), and Nitrospirae with (3.21 %). The metabolic functionality of the microbial communities present in the samples was inferred using the 16S rRNA amplicons. This work represents the first report of the microbial communities present in the Tecozautla geyser.

scholarly journals Passenger-surface microbiome interactions in the subway of Mexico City

2020 ◽  
Author(s):  
Daniela Vargas-Robles ◽  
Carolina Gonzalez-Cedillo ◽  
Apolinar M. Hernandez ◽  
Luis D. Alcaraz ◽  
Mariana Peimbert
Keyword(s):  
Microbial Diversity ◽  
Mexico City ◽  
16S Rrna Gene Sequencing ◽  
Surface Cleaning ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Usage Frequency ◽  
Rrna Gene Sequencing ◽  
Passenger Behavior ◽  
Effect Of Surface

AbstractInteraction between hands and the environment permits the interchange of microorganisms. The Mexico City subway is used daily by millions of passengers that get in contact with its surfaces. In this study, we used 16S rRNA gene sequencing to characterize the microbiomes of frequently touched surfaces, also comparing regular and women-only wagons. We also explored the effect of surface cleaning on microbial resettling. Finally, we studied passenger behavior and characterized microbial changes after traveling.Most passengers (99%), showed some type of surface interaction during a wagon trip, mostly with the hands (92%). We found microbiome differences associated with surfaces, probably reflecting diverse surface materials and usage frequency. The platform floor was the most bacterial diverse surface, while the stair handrail and pole were the least diverse ones. After pole cleaning, the resettling of microbial diversity was fast (5-30 minutes); however, it did not resemble the initial composition.After traveling, passengers significantly increased their hand microbial diversity and converged to a similar microbial composition among passengers. Additionally, passenger hand microbiomes resembled subway surfaces in diversity and also in the frequency of potentially pathogenic taxa. However, microbial fingerprints were preserved within passengers after traveling.

scholarly journals Gut Microbiome in Children from Indigenous and Urban Communities in México: Different Subsistence Models, Different Microbiomes

2020 ◽  
Vol 8 (10) ◽  
pp. 1592
Author(s):  
Andrés Sánchez-Quinto ◽  
Daniel Cerqueda-García ◽  
Luisa I. Falcón ◽  
Osiris Gaona ◽  
Santiago Martínez-Correa ◽  
...  
Keyword(s):  
Urban Communities ◽  
Mexico City ◽  
Gut Microbiome ◽  
Rrna Gene ◽  
High Fiber ◽  
Selective Pressures ◽  
Indigenous Group ◽  
Host Health ◽  
The 16S Rrna Gene ◽  
Total Diversity

The human gut microbiome is an important component that defines host health. Childhood is a particularly important period for the establishment and development of gut microbiota (GM). We sequenced the 16S rRNA gene from fecal samples of children between 5 and 10 years old, in two Mexican communities with contrasting lifestyles, i.e., “Westernized” (México City, n = 13) and “non-Westernized” (Me’phaa indigenous group, n = 29), in order to characterize and compare their GM. The main differences between these two communities were in bacteria associated with different types of diets (high animal protein and refined sugars vs. high fiber food, respectively). In addition, the GM of Me’phaa children showed higher total diversity and the presence of exclusive phyla, such as Deinococcus-Thermus, Chloroflexi, Elusimicrobia, Acidobacteria, and Fibrobacteres. In contrast, the children from México City showed less diversity and the presence of Saccharibacteria phylum, which was associated with the degradation of sugar compounds and was not present in the samples from Me’phaa children. This comparison provided further knowledge of the selective pressures affecting microbial ecosystemic composition over the course of human evolution and the potential consequences of pathophysiological states correlated with Westernization lifestyles.

scholarly journals The Microbial Community of Tetrodotoxin-Bearing and Non-Tetrodotoxin-Bearing Ribbon Worms (Nemertea) from the Sea of Japan

Marine Drugs ◽  
2020 ◽  
Vol 18 (3) ◽  
pp. 177 ◽  
Author(s):  
Daria I. Melnikova ◽  
Timur Yu. Magarlamov
Keyword(s):  
Bacterial Communities ◽  
Bacterial Species ◽  
Strong Support ◽  
Marine Ecosystems ◽  
The Sea Of Japan ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Marine Toxin ◽  
Gene Data ◽  
The 16S Rrna Gene

A potent marine toxin, tetrodotoxin (TTX), found in a great variety of marine and some terrestrial species, leaves intriguing questions about its origin and distribution in marine ecosystems. TTX-producing bacteria were found in the cultivable microflora of many TTX-bearing hosts, thereby providing strong support for the hypothesis that the toxin is of bacterial origin in these species. However, metagenomic studies of TTX-bearing animals addressing the whole microbial composition and estimating the contribution of TTX-producing bacteria to the overall toxicity of the host were not conducted. The present study is the first to characterize and compare the 16S rRNA gene data obtained from four TTX-bearing and four non-TTX-bearing species of marine ribbon worms. The statistical analysis showed that different nemertean species harbor distinct bacterial communities, while members of the same species mostly share more similar microbiomes. The bacterial species historically associated with TTX production were found in all studied samples but predominated in TTX-bearing nemertean species. This suggests that deeper knowledge of the microbiome of TTX-bearing animals is a key to understanding the origin of TTX in marine ecosystems.

scholarly journals Phylogenetic Diversity of Archaea in Shallow Hydrothermal Vents of Eolian Islands, Italy

Diversity ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 156 ◽  
Author(s):  
Concetta Gugliandolo ◽  
Teresa L. Maugeri
Keyword(s):  
Hydrothermal Vents ◽  
Inorganic Compounds ◽  
Archaeal Community ◽  
Hydrothermal Systems ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Vulcano Island ◽  
High Concentrations ◽  
Shallow Hydrothermal Vents ◽  
The 16S Rrna Gene

Shallow hydrothermal systems (SHS) around the Eolian Islands (Italy), related to both active and extinct volcanism, are characterized by high temperatures, high concentrations of CO2 and H2S, and low pH, prohibitive for the majority of eukaryotes which are less tolerant to the extreme conditions than prokaryotes. Archaea and bacteria are the key elements for the functioning of these ecosystems, as they are involved in the transformation of inorganic compounds released from the vent emissions and are at the basis of the hydrothermal system food web. New extremophilic archaea (thermophilic, hyperthermophilic, acidophilic, alkalophilic, etc.) have been isolated from vents of Vulcano Island, exhibiting interesting features potentially valuable in biotechnology. Metagenomic analyses, which mainly involved molecular studies of the 16S rRNA gene, provided different insights into microbial composition associated with Eolian SHS. Archaeal community composition at Eolian vent sites results greatly affected by the geochemistry of the studied vents, principally by hypersaline conditions and declining temperatures. Archaeal community in sediments was mostly composed by hyperthermophilic members of Crenarchaeota (class Thermoprotei) and Euryarchaeota (Thermococci and Methanococci) at the highest temperature condition. Mesophilic Euryarchaeota (Halobacteria, Methanomicrobia, and Methanobacteria) increased with decreasing temperatures. Eolian SHS harbor a high diversity of largely unknown archaea, and the studied vents may be an important source of new isolates potentially useful for biotechnological purposes.

scholarly journals Host Reproductive Cycle Influences the Pouch Microbiota of Wild Southern Hairy-Nosed Wombats (Lasiorhinus Latifrons)

2020 ◽  
Author(s):  
Sesilje Weiss ◽  
David Taggart ◽  
Ian Smith ◽  
Kristopher M Helgen ◽  
Raphael Eisenhofer
Keyword(s):  
16S Rrna ◽  
Reproductive Cycle ◽  
Tammar Wallaby ◽  
The Body ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Birth Canal ◽  
Negative Controls ◽  
Microbial Dna ◽  
The 16S Rrna Gene

Abstract Background: Marsupials are born much earlier than placental mammals, with most crawling from the birth canal to the protective marsupium (pouch) to further their development. However, little is known about the microbiology of the pouch and how it changes throughout a marsupial’s reproductive cycle. Here, using stringent controls, we characterized the microbial composition of multiple body sites from 26 wild Southern Hairy-nosed Wombats (SHNWs), including pouch samples from animals at different reproductive stages. Results: Using qPCR of the 16S rRNA gene we found higher concentrations of microbial DNA in the pouch than in negative controls. We observed significant differences in microbial composition and diversity between the body sites tested, as well as between pouch samples from different reproductive stages. Three of the five most abundant taxa identified in reproductively active pouches had closest matches to microbes previously isolated from tammar wallaby pouches. Conclusions: Our results suggest that SHNW pouches contain communities of microorganisms that are altered by the host reproductive cycle. We recommend further investigation into the roles that pouch microorganisms may play in marsupial reproductive health and joey survival.

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