scholarly journals Microbial Consortiums of Hydrogenotrophic Methanogenic Mixed Cultures in Lab-Scale Ex-Situ Biogas Upgrading Systems under Different Conditions of Temperature, pH and CO

2020 ◽  
Vol 8 (5) ◽  
pp. 772
Author(s):  
Jun Xu ◽  
Fan Bu ◽  
Wenzhe Zhu ◽  
Gang Luo ◽  
Li Xie
Keyword(s):  
Microbial Consortium ◽  
16S Rrna Gene Sequencing ◽  
Mixed Cultures ◽  
Ex Situ ◽  
Microbial Consortia ◽  
Rrna Gene ◽  
Biogas Upgrading ◽  
The Core ◽  
Rrna Gene Sequencing ◽  
Archaea Community

In this study, hydrogenotrophic methanogenic mixed cultures taken from 13 lab-scale ex-situ biogas upgrading systems under different temperature (20–70 °C), pH (6.0–8.5), and CO (0–10%, v/v) variables were systematically investigated. High-throughput 16S rRNA gene sequencing was used to identify the microbial consortia, and statistical analyses were conducted to reveal the microbial diversity, the core functional microbes, and their correlative relationships with tested variables. Overall, bacterial community was more complex than the archaea community in all mixed cultures. Hydrogenotrophic methanogens Methanothermobacter, Methanobacterium, and Methanomassiliicoccus, and putative syntrophic acetate-oxidizing bacterium Coprothermobacter and Caldanaerobacter were found to predominate, but the core functional microbes varied under different conditions. Multivariable sensitivity analysis indicated that temperature (p < 0.01) was the crucial variable to determine the microbial consortium structures in hydrogenotrophic methanogenic mixed cultures. pH (0.01 < p < 0.05) significantly interfered with the relative abundance of dominant archaea. Although CO did not affect community (p > 0.1), some potential CO-utilizing syntrophic metabolisms might be enhanced. Understanding of microbial consortia in the hydrogenotrophic methanogenic mixed cultures related to environmental variables was a great advance to reveal the microbial ecology in microbial biogas upgrading process.

Metataxonomics contributes to unravel the microbiota of a Brazilian dairy

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.

scholarly journals Contrasting gut microbiota in captive Eurasian otters (Lutra lutra) by age

2021 ◽  
Author(s):  
Yumiko Okamoto ◽  
Natsumi Ichinohe ◽  
Cheolwoon Woo ◽  
Sung-Yong Han ◽  
Hyeong-Hoo Kim ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
16S Rrna Gene Sequencing ◽  
Ex Situ ◽  
Conservation Strategies ◽  
Lutra Lutra ◽  
Rrna Gene ◽  
Baseline Information ◽  
The Difference ◽  
Rrna Gene Sequencing ◽  
And Function

AbstractUnderstanding the gut microbiota characteristics of endangered species such as the Eurasian otter (Lutra lutra), especially in their early stages of life, could be essential for improving their management and ex situ conservation strategies. Here, we analyzed the gut microbiota diversity, composition, and function of captive Eurasian otters at different ages using high-throughput 16S rRNA gene sequencing. We found that: (1) Clostridiaceae was abundant in all age stages; (2) Lactococcus in cubs is thought to predominate for digesting milk; (3) bacteria associated with amino acid metabolism increase with age, while bacteria associated with carbohydrate metabolism decrease with age, which is likely due to decrease in dietary carbohydrate content (e.g., milk) and increase in dietary protein contents (e.g., fishes) with age; and (4) fish-related bacteria were detected in feces of healthy adults and juveniles. Overall, the gut microbiota of captive Eurasian otters was taxonomically and functionally different by age, which is thought to be attributed to the difference in the diet in their life stages. This study provided baseline information regarding the gut microbiota of Eurasian otters for the first time and contributes to improvement in their management in captivity.

scholarly journals Evaluation of the Fecal Bacterial Communities of Angus Steers With Divergent Feed Efficiencies Across the Lifespan From Weaning to Slaughter

2021 ◽  
Vol 8 ◽  
Author(s):  
Christina B. Welch ◽  
Jeferson M. Lourenco ◽  
Taylor R. Krause ◽  
Darren S. Seidel ◽  
Francis L. Fluharty ◽  
...  
Keyword(s):  
Feed Efficiency ◽  
Microbial Consortium ◽  
16S Rrna Gene Sequencing ◽  
Production Cycle ◽  
Rrna Gene ◽  
Beef Steers ◽  
Dietary Changes ◽  
Fecal Microbiome ◽  
Gastrointestinal Bacteria ◽  
Rrna Gene Sequencing

Numerous studies have examined the link between the presence of specific gastrointestinal bacteria and the feed efficiency of cattle. However, cattle undergo dietary changes during their productive life which can cause fluctuations in their microbial consortium. The objective of the present study was to assess changes in the fecal microbiome of beef steers genetically selected to be divergent in feedlot feed efficiency, to determine whether differences in their fecal microbiomes could be detected as early as weaning, and continued throughout the rearing process regardless of dietary changes. Fecal samples were collected at weaning, yearling age, and slaughter for a group of 63 steers. Based on their feedlot-finishing performance, the steers were selected and divided into two groups according to their residual feed intake (RFI): efficient steers (low-RFI; n = 7) and inefficient steers (high-RFI; n = 8). To ascertain the fecal microbial consortium and volatile fatty acid (VFA) content, 16S rRNA gene sequencing and VFA analysis were performed. Overall, bacterial evenness and diversity were greater at weaning compared to yearling and slaughter for both efficiency groups (P &lt; 0.001). Feedlot RFI linearly decreased as both Shannon diversity and Ruminococcaceae abundance increased (R2 = 65.6 and 60.7%, respectively). Abundances of Ruminococcaceae, Rikenellaceae, and Christensenellaceae were higher at weaning vs. yearling age and slaughter (P &lt; 0.001); moreover, these families were consistently more abundant in the feces of the low-RFI steers (for most of the timepoints evaluated; P ≤ 0.05), compared to the high-RFI steers. Conversely, abundances of Bifidobacteriaceae were numerically higher in the feces of the high-RFI steers throughout their lifespan. Total VFA concentrations increased at slaughter compared to weaning and yearling for both efficiency groups (P &lt; 0.001). The acetate:propionate ratio decreased linearly (P &lt; 0.001) throughout the life of the steers regardless of their efficiency, reflective of dietary changes. Our results indicate that despite fluctuations due to animal age and dietary changes, specific bacterial families may be correlated with feed efficiency of steers. Furthermore, such differences may be identifiable at earlier stages of the production cycle, potentially as early as weaning.

scholarly journals Temperature Responses of Heterotrophic Bacteria in Co-culture With a Red Sea Synechococcus Strain

2021 ◽  
Vol 12 ◽  
Author(s):  
Abbrar Labban ◽  
Antonio S. Palacio ◽  
Francisca C. García ◽  
Ghaida Hadaidi ◽  
Mohd I. Ansari ◽  
...  
Keyword(s):  
Red Sea ◽  
Heterotrophic Bacteria ◽  
16S Rrna Gene Sequencing ◽  
Microbial Consortia ◽  
Rrna Gene ◽  
Different Temperatures ◽  
Synechococcus Strain ◽  
Rrna Gene Sequencing ◽  
Taxonomic Affiliation ◽  
Specific Growth Rates

Interactions between autotrophic and heterotrophic bacteria are fundamental for marine biogeochemical cycling. How global warming will affect the dynamics of these essential microbial players is not fully understood. The aims of this study were to identify the major groups of heterotrophic bacteria present in a Synechococcus culture originally isolated from the Red Sea and assess their joint responses to experimental warming within the metabolic ecology framework. A co-culture of Synechococcus sp. RS9907 and their associated heterotrophic bacteria, after determining their taxonomic affiliation by 16S rRNA gene sequencing, was acclimated and maintained in the lab at different temperatures (24–34°C). The abundance and cellular properties of Synechococcus and the three dominant heterotrophic bacterial groups (pertaining to the genera Paracoccus, Marinobacter, and Muricauda) were monitored by flow cytometry. The activation energy of Synechococcus, which grew at 0.94–1.38 d–1, was very similar (0.34 ± 0.02 eV) to the value hypothesized by the metabolic theory of ecology (MTE) for autotrophs (0.32 eV), while the values of the three heterotrophic bacteria ranged from 0.16 to 1.15 eV and were negatively correlated with their corresponding specific growth rates (2.38–24.4 d–1). The corresponding carrying capacities did not always follow the inverse relationship with temperature predicted by MTE, nor did we observe a consistent response of bacterial cell size and temperature. Our results show that the responses to future ocean warming of autotrophic and heterotrophic bacteria in microbial consortia might not be well described by theoretical universal rules.

scholarly journals Alterations of Thyroid Microbiota Across Different Thyroid Microhabitats in Patients With Thyroid Carcinoma

2021 ◽  
Author(s):  
Daofeng Dai ◽  
Yang Yan ◽  
Yong Yang ◽  
Tianfeng Dang ◽  
Jiansheng Xiao ◽  
...  
Keyword(s):  
Thyroid Carcinoma ◽  
Incidence Rate ◽  
Area Under The Curve ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
The Core ◽  
Node Metastasis ◽  
Tumor Tissues ◽  
Rrna Gene Sequencing

Abstract Background: In recent years, the incidence rate of Thyroid carcinoma(TC) has been increasing worldwide. Thus, research on factors of TC carcinogenesis may promote TC prevention and decrease the incidence rate. There are several studies targeting the correlation between gut microbiota and thyroid disease. Carcinogenesis of several malignancies is influenced by microbiota. However, thyroid microbiome of TC has not been revealed. This study investigated thyroid microbiota in different TC microhabitats. Methods: We performed 16s rRNA gene sequencing using tumor tissues and matched peritumor tissues from 30 patients with TC to characterize thyroid microbiota. Results: The richness and diversity of thyroid microbiota were lower in TC tumor samples than in matched peritumor tissues. At the genus level, the core microbiota of thyroid included Sphingomonas, Comamonas, Acinetobacter, Pseudomonas, Microvirgula, and Soonwooa. The abundance of Sphingomonas and Aeromonas was significantly increased in tumor tissues, while the abundance of Comamonas, Acinetobacter, and Peptostreptococcus was significantly enhanced in peritumor tissues. The combination of Comamonas and Sphingomonas could discriminate tumor samples from peritumor samples with an area under the curve (AUC) of 0.981 (95% confidence interval [CI]: 0.949-1.000). The abundance of Sphingomonas was significantly higher in N1 stage than in N0 stage. Sphingomonas could distinguish between N0 and N1 stage with an AUC of 0.964 (95% CI: 0.907-1.000).Conclusions: The microbial diversity and composition were significantly different between peritumor and tumor microhabitats from patients with TC, which may eventually affect TC carcinogenesis and progression. The combination of Comamonas and Sphingomonas could serve as a powerful biomarker for discrimination between tumor and peritumor tissues. Furthermore, the higher abundance of Sphingomonas was correlated with lymph node metastasis, indicating that it may play a role in promoting TC progression.

scholarly journals Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia

2016 ◽  
Vol 113 (28) ◽  
pp. E4069-E4078 ◽  
Author(s):  
Roland Hatzenpichler ◽  
Stephanie A. Connon ◽  
Danielle Goudeau ◽  
Rex R. Malmstrom ◽  
Tanja Woyke ◽  
...  
Keyword(s):  
16S Rrna Gene Sequencing ◽  
Microbial Consortia ◽  
Rrna Gene ◽  
Anaerobic Oxidation Of Methane ◽  
Bacterial Consortia ◽  
Symbiotic Relationships ◽  
Oxidation Of Methane ◽  
Translational Activity ◽  
Rrna Gene Sequencing

To understand the biogeochemical roles of microorganisms in the environment, it is important to determine when and under which conditions they are metabolically active. Bioorthogonal noncanonical amino acid tagging (BONCAT) can reveal active cells by tracking the incorporation of synthetic amino acids into newly synthesized proteins. The phylogenetic identity of translationally active cells can be determined by combining BONCAT with rRNA-targeted fluorescence in situ hybridization (BONCAT-FISH). In theory, BONCAT-labeled cells could be isolated with fluorescence-activated cell sorting (BONCAT-FACS) for subsequent genetic analyses. Here, in the first application, to our knowledge, of BONCAT-FISH and BONCAT-FACS within an environmental context, we probe the translational activity of microbial consortia catalyzing the anaerobic oxidation of methane (AOM), a dominant sink of methane in the ocean. These consortia, which typically are composed of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria, have been difficult to study due to their slow in situ growth rates, and fundamental questions remain about their ecology and diversity of interactions occurring between ANME and associated partners. Our activity-correlated analyses of >16,400 microbial aggregates provide the first evidence, to our knowledge, that AOM consortia affiliated with all five major ANME clades are concurrently active under controlled conditions. Surprisingly, sorting of individual BONCAT-labeled consortia followed by whole-genome amplification and 16S rRNA gene sequencing revealed previously unrecognized interactions of ANME with members of the poorly understood phylum Verrucomicrobia. This finding, together with our observation that ANME-associated Verrucomicrobia are found in a variety of geographically distinct methane seep environments, suggests a broader range of symbiotic relationships within AOM consortia than previously thought.

scholarly journals Microbial Community Succession is Associated With Corn Straw Degradation in Microbial Consortium M44 During Subculture

2021 ◽  
Author(s):  
Xin ZHANG ◽  
Ge-Er QING ◽  
Ju-Lin GAO ◽  
Xiao-Fang YU ◽  
Shu-Ping HU ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
16S Rrna Gene Sequencing ◽  
Microbial Consortia ◽  
Rrna Gene ◽  
Original Sample ◽  
Microbial Composition ◽  
Endoglucanase Activity ◽  
Rrna Gene Sequencing

Abstract To systematically analyze the succession of functional microbiota that plays an important role during culture of microbial consortia M44 and its relationship with straw degradation characteristics, we determined the straw degradation ratio and activities of cellulose, hemicellulose, lignin enzyme, and VFA content of M44 in different culture periods. We also used 16S rRNA gene sequencing to analyze the change in microbial community structure in M44 and explore the differences in microbial composition in the original sample. The results showed that at 15 ℃ for 21 days, the straw degradation rate, endoglucanase activity, and filter paper enzyme activity of M44 generally decreased with increasing culture age, reaching their highest values at F1. The activities of xylanase, laccase, and lignin peroxidase, as well as VFA content, were the highest at F5, showing a single-peak curve change with first an increase and then decrease. At the phylum level, Proteobacteria, Bacteroidetes, and Firmicutes were dominant in the original samples and in different culture stages. At the genus level, Devosia and Bacillus were dominant in the original sample. During subculture, the dominant bacteria in the first generation (F1) were Pseudomonas, Flavobacterium, Brevundimonas, Achromobacter, Chryseobacterium, and Devosia. The dominant genera in the last generation (F11) were Trichococcus, Acinetobacter, Dyssgonomonas, and Rhizobium. In conclusion, we identified changes in microbial community structure occurring in M44 during subculture, as well as similarities and differences in microbial communities from the original sample.

scholarly journals Alterations of thyroid microbiota across different thyroid microhabitats in patients with thyroid carcinoma

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Daofeng Dai ◽  
Yan Yang ◽  
Yong Yang ◽  
Tianfeng Dang ◽  
Jiansheng Xiao ◽  
...  
Keyword(s):  
Thyroid Carcinoma ◽  
Incidence Rate ◽  
Area Under The Curve ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
The Core ◽  
Node Metastasis ◽  
Tumor Tissues ◽  
Rrna Gene Sequencing

Abstract Background In recent years, the incidence rate of Thyroid carcinoma (TC) has been increasing worldwide. Thus, research on factors of TC carcinogenesis may promote TC prevention and decrease the incidence rate. There are several studies targeting the correlation between gut microbiota and thyroid disease. Carcinogenesis of several malignancies is influenced by microbiota. However, thyroid microbiome of TC has not been revealed. This study investigated thyroid microbiota in different TC microhabitats. Methods We performed 16s rRNA gene sequencing using tumor tissues and matched peritumor tissues from 30 patients with TC to characterize thyroid microbiota. Results The richness and diversity of thyroid microbiota were lower in TC tumor samples than in matched peritumor tissues. At the genus level, the core microbiota of thyroid included Sphingomonas, Comamonas, Acinetobacter, Pseudomonas, Microvirgula, and Soonwooa. The abundance of Sphingomonas and Aeromonas was significantly increased in tumor tissues, while the abundance of Comamonas, Acinetobacter, and Peptostreptococcus was significantly enhanced in peritumor tissues. The combination of Comamonas and Sphingomonas could discriminate tumor samples from peritumor samples with an area under the curve (AUC) of 0.981 (95% confidence interval [CI] 0.949–1.000). The abundance of Sphingomonas was significantly higher in N1 stage than in N0 stage. Sphingomonas could distinguish between N0 and N1 stage with an AUC of 0.964 (95% CI 0.907–1.000). Conclusions The microbial diversity and composition were significantly different between peritumor and tumor microhabitats from patients with TC, which may eventually affect TC carcinogenesis and progression. The combination of Comamonas and Sphingomonas could serve as a powerful biomarker for discrimination between tumor and peritumor tissues. Furthermore, the higher abundance of Sphingomonas was correlated with lymph node metastasis, indicating that the abundance of Sphingomonas may indicate a poor prognosis for TC patients, and Sphingomonas may play a role in promoting TC progression.

Unravelling a microbial synergy to boost caproate production via carboxylates chain elongation with ethanol

2019 ◽  
Vol 26 (2) ◽  
pp. 63-71
Author(s):  
Ling Leng ◽  
Ying Wang ◽  
Peixian Yang ◽  
Takashi Narihiro ◽  
Masaru Konishi Nobu ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Volatile Fatty Acids ◽  
Microbial Consortia ◽  
Chain Elongation ◽  
Desulfovibrio Vulgaris ◽  
Rrna Gene ◽  
Selective Enrichment ◽  
Microbial Network ◽  
Cost Efficient ◽  
Rrna Gene Sequencing

Chain elongation of volatile fatty acids for medium chain fatty acids production (e.g. caproate) is an attractive approach to treat wastewater anaerobically and recover resource simultaneously. Undefined microbial consortia can be tailored to achieve chain elongation process with selective enrichment from anaerobic digestion sludge, which has advantages over pure culture approach for cost-efficient application. Whilst the metabolic pathway of the dominant caproate producer, Clostridium kluyveri, has been annotated, the role of other coexisting abundant microbiomes remained unclear. To this end, an ethanol-acetate fermentation inoculated with fresh digestion sludge at optimal conditions was conducted. Also, physiological study, thermodynamics and 16 S rRNA gene sequencing to elucidate the biological process by linking the system performance and dominant microbiomes were integrated. Results revealed a possible synergistic network in which C. kluyveri and three co-dominant species, Desulfovibrio vulgaris, Fusobacterium varium and Acetoanaerobium sticklandii coexisted. D. vulgaris and A. sticklandii (F. varium) were likely to boost the carboxylates chain elongation by stimulating ethanol oxidation and butyrate production through a syntrophic partnership with hydrogen (H2) serving as an electron messenger. This study unveils a synergistic microbial network to boost caproate production in mixed culture carboxylates chain elongation.

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