scholarly journals Fecal microbiota and their association with heat stress in Bos taurus

2021 ◽  
Author(s):  
Batosz Czech ◽  
Joanna Szyda ◽  
Kai Wang ◽  
Hanpeng Luo ◽  
Yachun Wang
Keyword(s):  
Heat Stress ◽  
16S Rrna ◽  
Fossil Fuels ◽  
Negative Binomial ◽  
Bos Taurus ◽  
Sequence Data ◽  
16S Rrna Gene Sequencing ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Stress Changes

Humans have been influencing climate changes by burning fossil fuels, farming livestock, and cutting down rainforests, which has led to global temperature rise. This problem of global warming affects animals by causing heat stress, which negatively affects their health, biological functions, and reproduction. On the molecular level, it has been proved that heat stress changes the expression level of genes and therefore causes changes in proteome and metabolome. The importance of a microbiome in many studies showed that it is considered as individuals' 'second genome'. Physiological changes caused by heat stress may impact the microbiome composition. In this study, we identified fecal microbiota associated with heat stress that was quantified by three metrics - rectal temperature, drooling, and respiratory scores and represented by their Estimated Breeding Values. For this purpose, the 16S rRNA sequencing technique was used. We analyzed the microbiota from 136 fecal samples of Chinese Holstein cows through a 16S rRNA gene sequencing approach. Sequence data were processed using a pipeline involving QIIME2 software together with SILVA database. Statistical modeling was performed using a negative binomial regression. The analysis revealed the total number of 24 genera and 12 phyla associated with heat stress metrics. Rhizobium and Pseudobutyrivibrio turned out to be the most significant genera, while Acidobacteria and Gemmatimonadetes were the most significant phyla. Phylogenetic analysis revealed that that three heat stress indicators quantify different metabolic ways of animals' reaction to heat stress. Other studies already identified that those genera had significantly increased abundance in mice exposed to stressor-induced changes. Moreover, identified microbiota significantly associated with heat stress measures were mostly mesophilic, so their association seems to be due to heat stress-induced secondary, metabolic changes, and not directly by temperature. Moreover, high fold changes of many genera suggest that they may be used as biomarkers for monitoring the level of heat stress in cattle.

scholarly journals Fecal Microbiota and Their Association With Heat Stress in Bos Taurus

2021 ◽  
Author(s):  
Bartosz Czech ◽  
Joanna Szyda ◽  
Kai Wang ◽  
Hanpeng Luo ◽  
Yachun Wang
Keyword(s):  
Heat Stress ◽  
16S Rrna ◽  
Negative Binomial ◽  
Sequence Data ◽  
16S Rrna Gene Sequencing ◽  
Continuous Variable ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Microbiome Composition ◽  
Stress Changes

Abstract Background: Humans have been influencing climate changes by burning fossil fuels, farming livestock, and cutting down rainforests, which has led to global temperature rise. This problem of global warming affects animals by causing heat stress, which negatively affects their health, biological functions, and reproduction. On the molecular level, it has been proved that heat stress changes the expression level of genes and therefore causes changes in proteome and metabolome. The importance of a microbiome in many studies showed that it is considered as individuals’ “second genome”. Physiological changes caused by heat stress may impact the microbiome composition. Results: In this study, we identified fecal microbiota associated with heat stress that was quantified by three metrics – rectal temperature, drooling, and respiratory scores and represented by their Estimated Breeding Values. For this purpose, the 16S rRNA sequencing technique was used. We analyzed the microbiota from 136 fecal samples of Chinese Holstein cows through a 16S rRNA gene sequencing approach. Sequence data were processed using a pipeline involving QIIME2 software together with SILVA database. Statistical modeling was performed using a negative binomial regression. The analysis revealed the total number of 24 genera and 12 phyla associated with heat stress metrics. Rhizobium and Pseudobutyrivibrio turned out to be the most significant genera, while Acidobacteria and Gemmatimonadetes were the most significant phyla. Phylogenetic analysis revealed that that three heat stress indicators quantify different metabolic ways of animals’ reaction to heat stress. Other studies already identified that those genera had significantly increased abundance in mice exposed to stressor-induced changes. Conclusions: This study provides insights into the analysis of microbiome composition in cattle using heat stress measured as a continuous variable. The bacteria highly associated with heat stress were highlighted and can be used as biomarkers in further microbiological studies.

scholarly journals Prokaryotic taxonomy in the sequencing era and the role of MLSA in classification

2011 ◽  
Vol 32 (2) ◽  
pp. 66 ◽  
Author(s):  
Peter Kampfer ◽  
Stefanie P Glaeser
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
16S Rrna Gene Sequencing ◽  
Initial Step ◽  
Rrna Gene ◽  
Sequence Analyses ◽  
Phenotypic Characterisation ◽  
Novel Taxa ◽  
Rrna Gene Sequencing

The initial step in prokaryote species and genera descriptions is now largely based on the 16S rRNA gene sequencing approach followed often by a very restricted additional phenotypic characterisation of the representatives of the potential novel taxa. Despite the advantages of the sequence-based approaches, there appears to be a tendency to classify new species on the basis of comparative sequence analyses of 16S rRNA gene sequences and other gene sequence data (multilocus sequence analyses, MLSA), contrary to the indications of other data. However, the biological meaning behind these sequence data is not always clear, and one should be careful with comprehensive taxonomic rearrangements until there is better insight of these data.

scholarly journals 16S rRNA Gene Amplicon Sequence Data from Feces of Five Species of Wild Animals in Japan

2020 ◽  
Vol 9 (22) ◽  
Author(s):  
Kasumi Ishida-Kuroki ◽  
Nachiko Takeshita ◽  
Yoshihiro Nitta ◽  
Takehisa Chuma ◽  
Ken Maeda ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Animal Species ◽  
Sequence Data ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Wild Animals ◽  
Wild Boars ◽  
Raccoon Dogs

ABSTRACT We report 16S rRNA amplicon sequence data from feces from 58 wild boars, 60 feral raccoons, 9 wild Japanese badgers, 21 wild masked palm civets, and 8 wild raccoon dogs in Japan. The predominant bacterial taxa in the fecal microbiota were similar in part but varied among the animal species.

scholarly journals Introducing an Environmental Microbiome to Axenic Insectary Reared Mosquitoes Alters Host and Microbe Blood Digestion Phenotypes

2021 ◽  
Author(s):  
Blaire Steven ◽  
Jacquelyn LaReau ◽  
Josephine Hyde ◽  
Doug Brackney
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Blood Meal ◽  
Temporal Dynamics ◽  
Sequence Data ◽  
16S Rrna Gene Sequencing ◽  
Water Source ◽  
Environmental Water ◽  
Rrna Gene ◽  
Blood Digestion

Abstract The microbiota of Aedes aegypti has been the subject of much research due to the potential role of the microbiome in mosquito physiology, development, and vectorial capacity. Axenic mosquitoes were colonized with environmental bacteria to compare microbiota acquired from the environment to insectary reared counterparts, particularly regarding blood meal digestion. Observationally, environmentally colonized mosquitoes showed faster blood digestion than insectary mosquitoes. 16S rRNA gene sequencing revealed that the diversity and community structure of the midgut microbiomes were distinct between the groups, with the environmental microbiomes having a greater diversity and larger temporal dynamics over the course of the blood meal. Metagenomic prediction from the 16S rRNA gene sequence data pointed to functional genes such as hemolysins differing between the two microbiomes. Additionally, only bacteria cultured from the environmental mosquitoes demonstrated hemolytic ability. Presence of these hemolytic bacteria may explain the observations of differing blood digestion rates in the mosquito. These data show that microbiomes of mosquitoes colonized from an environmental water source differ taxonomically and functionally from those from the insectary, with potential influences on host blood digestion. Thus, the axenic mosquito model can be employed to interrogate various microbiome compositions and link them to phenotypic outcomes of the host.

scholarly journals 16S rRNA Gene Amplicon Sequence Data from Feces of Wild Deer (Cervus nippon) in Japan

2020 ◽  
Vol 9 (22) ◽  
Author(s):  
Kasumi Ishida-Kuroki ◽  
Nachiko Takeshita ◽  
Yoshihiro Nitta ◽  
Takehisa Chuma ◽  
Ken Maeda ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Cervus Nippon ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Mountainous Areas ◽  
Wild Deer

ABSTRACT We report 16S rRNA amplicon sequence data from feces of 109 wild deer in Japan. The dominant bacterial taxa in fecal microbiota of wild deer hunted between village and mountainous areas and those living on Miyajima Island and in Nara Park were similar but differed in abundance.

Saccharomyces cerevisiae boulardii CNCM I-1079 supplementation in finishing male pigs helps to cope with heat stress through feeding behavior and gut microbiota modulation

2021 ◽  
pp. 1-35
Author(s):  
E. Labussière ◽  
C.S. Achard ◽  
S. Dubois ◽  
S. Combes ◽  
M. Castex ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Heat Stress ◽  
Feeding Behavior ◽  
Feed Intake ◽  
Keystone Species ◽  
16S Rrna Gene Sequencing ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Energy Retention

Abstract Pigs subjected to heat stress (HS) decrease their feed intake and growth. The objectives of the experiment were to determine the effects of live yeast (LY) supplementation (Saccharomyces cerevisiae var boulardii CNCM I-1079) on feeding behavior, energy metabolism and fecal microbiota composition of finishing boars (n=10) housed in respiration chamber at thermoneutrality (seven days at 22°C) or during HS (seven plus six days at 28°C). Dietary LY supplementation increased dry matter intake (P = 0.01), whatever the ambient temperature, whereas HS decreased feed intake whatever dietary supplementation (P = 0.01). Dietary LY supplementation increased the number of meals (P = 0.02). Energy retention was higher with dietary LY supplementation (P < 0.01) but decreased during HS (P < 0.01). The skin temperature of the supplemented pigs was lower at thermoneutrality and increased during HS to a lesser extent than that of non-supplemented pigs (P < 0.01). Fecal microbiota composition was determined using 16S rRNA gene sequencing. Treponema, Christensenellaceae R-7, Ruminococcaceae UCG-002, Rikenellaceae RC9, Clostridium sensu stricto 1 and Romboutsia genera and some bacteria belonging to Alloprevotella, Oxalobacter and Anaeroplasma genera were more abundant under HS. LY supplementation attenuated HS effects on Romboutsia abundance, while decreasing the abundance of some bacteria from Ruminoccocus, Coprococcus, Peptococcus and Oxalobacter genera and increasing the abundance of beneficial bacteria from Lactococcus and Subdoligranulum genera. Our results suggest that higher level of the keystone species Ruminococcus Bromii at thermoneutrality may be one of the cause for higher energy retention observed under subsequent HS.

scholarly journals Phaeodactylibacter luteus sp. nov., isolated from the oleaginous microalga Picochlorum sp.

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2666-2670 ◽  
Author(s):  
Xueqian Lei ◽  
Yi Li ◽  
Guanghua Wang ◽  
Yao Chen ◽  
Qiliang Lai ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sequence Data ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Biodiesel Production ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
Respiratory Quinone ◽  
Gram Staining ◽  
Rrna Gene Sequencing

A Gram-staining-negative, orange-pigmented, non-motile, aerobic bacterial strain, designated GYP20T, was isolated from a culture of the alga Picochlorum sp., a promising feedstock for biodiesel production, which was isolated from the India Ocean. Growth was observed at temperatures from 20 to 37 °C, salinities from 0 to 3  % and pH from 5 to 9.Mg 2+ and Ca2+ ions were required for growth. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the strain was a member of the genus Phaeodactylibacter, which belongs to the family Saprospiraceae. Strain GYP20T was most closely related to Phaeodactylibacter xiamenensis KD52T (95.5  % sequence similarity). The major fatty acids were iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3. The predominant respiratory quinone was menaquinone-7 (MK-7). The polar lipids of strain GYP20T were found to consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, four unidentified glycolipids, two unidentified phospholipids and three unidentified aminolipids. According to its morphology, physiology, fatty acid composition and 16S rRNA sequence data, the novel strain most appropriately belongs to the genus Phaeodactylibacter, but can readily be distinguished from Phaeodactylibacter xiamenensis GYP20T. The name Phaeodactylibacter luteus sp. nov. is proposed with the type strain GYP20T ( = MCCC 1F01222T = KCTC 42180T).

scholarly journals Discrete Community Assemblages Within Hypersaline Paleolake Sediments of Pilot Valley, Utah

2019 ◽  
Author(s):  
Kennda L. Lynch ◽  
Kevin A. Rey ◽  
Robin J. Bond ◽  
Jennifer F. Biddle ◽  
John R. Spear ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
16S Rrna Gene Sequencing ◽  
Small Subunit ◽  
Rrna Gene ◽  
Sediment Grain Size ◽  
Bacterial Phyla ◽  
Rrna Gene Sequencing ◽  
Biogeochemical Parameters

AbstractHypersaline paleolake sediments are understudied ecosystems whose microbial ecology is largely unknown. Here we present mineralogical, geochemical, and small-subunit 16S rRNA gene sequence data on one such environment, the Pilot Valley Basin (PVB), a sub-basin of ancient Lake Bonneville located in northwest Utah. PVB exhibits a variety of aqueous minerals including phyllosilicates, carbonates, and sulfates, as well as microbially-induced sedimentary structures. As perchlorate occurs naturally (up to 6.5 ppb) in Pilot Valley sediments, and because recent evidence suggests that it is subject to biotic reduction, PVB has been proposed as a Mars analog site for astrobiological studies. 16S rRNA gene sequencing was used to investigate microbial diversity and community structure along horizontal and vertical transects within the upper basin sediments and beta diversity analyses indicate that the microbial communities in Pilot Valley are structured into three discrete groups.Operational taxonomicunits (OTUs) belonging to the main archaeal phylum, Euryarchaeota, make up ~23% of the sequences, while OTUs belonging to three bacterial phyla, Proteobacteria, Bacteroides and Gemmatimonadetes, constitute ~60-70% of the sequences recovered at all sites. Diversity analyses indicate that the specific composition of each community correlates with sediment grain size, and with biogeochemical parameters such as nitrate and sulfate concentrations. Interestingly, OTUs belonging to the phylum Gemmatimonadetes are co-located with extreme halophilic archaeal and bacterial taxa, which suggests a potential new attribute, halophilicity, of this newly-recognized phylum. Altogether, results of this first comprehensive geomicrobial study of Pilot Valley reveal that basin sediments harbor a complex and diverse ecosystem.

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