core microbiome
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2022 ◽  
Vol 12 ◽  
Author(s):  
Marie-Amélie Blais ◽  
Alex Matveev ◽  
Connie Lovejoy ◽  
Warwick F. Vincent

Little is known about the microbial diversity of rivers that flow across the changing subarctic landscape. Using amplicon sequencing (rRNA and rRNA genes) combined with HPLC pigment analysis and physicochemical measurements, we investigated the diversity of two size fractions of planktonic Bacteria, Archaea and microbial eukaryotes along environmental gradients in the Great Whale River (GWR), Canada. This large subarctic river drains an extensive watershed that includes areas of thawing permafrost, and discharges into southeastern Hudson Bay as an extensive plume that gradually mixes with the coastal marine waters. The microbial communities differed by size-fraction (separated with a 3-μm filter), and clustered into three distinct environmental groups: (1) the GWR sites throughout a 150-km sampling transect; (2) the GWR plume in Hudson Bay; and (3) small rivers that flow through degraded permafrost landscapes. There was a downstream increase in taxonomic richness along the GWR, suggesting that sub-catchment inputs influence microbial community structure in the absence of sharp environmental gradients. Microbial community structure shifted across the salinity gradient within the plume, with changes in taxonomic composition and diversity. Rivers flowing through degraded permafrost had distinct physicochemical and microbiome characteristics, with allochthonous dissolved organic carbon explaining part of the variation in community structure. Finally, our analyses of the core microbiome indicated that while a substantial part of all communities consisted of generalists, most taxa had a more limited environmental range and may therefore be sensitive to ongoing change.


Author(s):  
Brook A. Niemiec ◽  
Jerzy Gawor ◽  
Shuiquan Tang ◽  
Aishani Prem ◽  
Janina A. Krumbeck

Abstract OBJECTIVE To compare the bacteriome of the oral cavity in healthy dogs and dogs with various stages of periodontal disease. ANIMALS Dogs without periodontal disease (n = 12) or with mild (10), moderate (19), or severe (10) periodontal disease. PROCEDURES The maxillary arcade of each dog was sampled with a sterile swab, and swabs were submitted for next-generation DNA sequencing targeting the V1–V3 region of the 16S rRNA gene. RESULTS 714 bacterial species from 177 families were identified. The 3 most frequently found bacterial species were Actinomyces sp (48/51 samples), Porphyromonas cangingivalis (47/51 samples), and a Campylobacter sp (48/51 samples). The most abundant species were P cangingivalis, Porphyromonas gulae, and an undefined Porphyromonas sp. Porphyromonas cangingivalis and Campylobacter sp were part of the core microbiome shared among the 4 groups, and P gulae, which was significantly enriched in dogs with severe periodontal disease, was part of the core microbiome shared between all groups except dogs without periodontal disease. Christensenellaceae sp, Bacteroidales sp, Family XIII sp, Methanobrevibacter oralis, Peptostreptococcus canis, and Tannerella sp formed a unique core microbiome in dogs with severe periodontal disease. CONCLUSIONS AND CLINICAL RELEVANCE Results highlighted that in dogs, potential pathogens can be common members of the oral cavity bacteriome in the absence of disease, and changes in the relative abundance of certain members of the bacteriome can be associated with severity of periodontal disease. Future studies may aim to determine whether these changes are the cause or result of periodontal disease or the host immune response.


2021 ◽  
Author(s):  
Claire A Woodall ◽  
Ashley Hammond ◽  
David W Cleary ◽  
Andrew Preston ◽  
Peter Muir ◽  
...  

Abstract Background and aim: Respiratory tract infections (RTIs) are common in the community. There is some evidence that microbial biomarkers can be used to identify individuals most susceptible to RTI acquisition. We investigated the feasibility of recruiting healthy adults to collect at-home self-reported socio-demographic data and biological samples, saliva (oral) and stool (gut) at three time points (TPs): baseline/start of the study (TP-A), during an RTI (TP-B) and end of study (TP-C). Methods: Healthy adults were recruited from two urban Bristol GP practices. To identify respiratory pathogens in all saliva samples and RTI-S stool samples reverse transcriptase PCR (RT-PCR) was applied. We compared oral and gut samples from participants who developed RTI symptoms (RTI-S) and those who remained healthy (no-RTI) using 16S rRNA profiling microbiome analysis to identify the core microbiome, alpha and beta diversity, and biomarkers for susceptibility to RTIs from baseline samples (TP-A) when all participants were healthy. Results: We recruited 56 participants but due to the UK COVID-19 pandemic disruption we did not receive samples from 16 participants leaving 19 RTI-S and 21 no-RTI participants with socio-demographic and microbiome data. RT-PCR revealed coagulase-negative Staphylococcus carriage was significantly higher in RTI-S participants compared to those who remained healthy and RTI symptoms may have been due to viral influenzae and bacterial co-infection with Haemophilus influenzae. Core microbiomes of no-RTI participants contained a greater number of taxa compared to RTI-S participants. Microbial biomarkers of RTI susceptibility in the oral cavity were an increased abundance of the pathobiont Streptococcus sobrinus and decreased probiotic bacterium Lactobacillus salivarius whereas in the gut there was an increased abundance of the genus Veillonella and decreased abundance of Coprobacillus. Conclusion: In our feasibility study we found oral and gut microbial biomarkers for susceptibility to RTI acquisition. Strategies to identify those most vulnerable to RTI in the community could lead to novel interventions to decrease respiratory infection and associated health services burden.


Author(s):  
Daphne Perlman ◽  
Marina Martínez-Álvaro ◽  
Sarah Moraïs ◽  
Ianina Altshuler ◽  
Live H. Hagen ◽  
...  

Animal microbiomes are occasionally considered as an extension of host anatomy, physiology, and even their genomic architecture. Their compositions encompass variable and constant portions when examined across multiple hosts. The latter, termed the core microbiome, is viewed as more accommodated to its host environment and suggested to benefit host fitness. Nevertheless, discrepancies in its definitions, characteristics, and importance to its hosts exist across studies. We survey studies that characterize the core microbiome, detail its current definitions and available methods to identify it, and emphasize the crucial need to upgrade and standardize the methodologies among studies. We highlight ruminants as a case study and discuss the link between the core microbiome and host physiology and genetics, as well as potential factors that shape it. We conclude with main directives of action to better understand the host–core microbiome axis and acquire the necessary insights into its controlled modulation. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.


2021 ◽  
Author(s):  
Alexis Gkantiragas ◽  
Jacopo Gabrielli

Honeybees (Apis Mellifera) perform an essential role in the ecosystem and economy through pollination of insect-pollinated plants, but their population is declining. Many causes of honeybees' decline are likely to be influenced by the microbiome which is thought to play an important role in bees and is particularly susceptible to infection and pesticides. However, there has been no systematic review or meta-analysis on honeybee microbiome data. Therefore, we conducted the first systematic meta-analysis of 16S-rRNA data to address this gap in the literature. Four studies were in a usable format - accounting for 336 honeybee's worth of data - the largest such dataset to the best of our knowledge. We analysed these datasets in QIIME2 and visualised the results in R-studio. For the first time, we conducted a multi-study evaluation of the core and rare bee microbiome and confirmed previous compositional microbiome data. We established that Snodgrassella, Lactobacillus, Bifidobacterium, Fructobacillus and Saccaribacter form part of the core microbiome and identify 251 rare bacterial genera. Additional components of the core microbiome were likely obscured by incomplete classification. Future studies should refine and add to our existing dataset to produce a more conclusive and high-resolution portrait of the honeybee microbiome. Furthermore, we emphasise the need for an actively curated dataset and enforcement of data sharing standards.


2021 ◽  
Vol 12 ◽  
Author(s):  
Jing Zhu ◽  
Xiang Sun ◽  
Qi-Yong Tang ◽  
Zhi-Dong Zhang

Endophytes are essential components of plant microbiota. Studies have shown that environmental factors and seasonal alternation can change the microbial community composition of plants. However, most studies have mainly emphasized the transitive endophyte communities and seasonal alternation but paid less attention to their persistence through multiple seasons. Kalidium schrenkianum is a perennial halophyte growing in an arid habitat with radiation stress (137Cs) in northwest China. In this study, K. schrenkianum growing under different environmental stresses were selected to investigate the dynamics and persistency of endophytic microbial communities amid seasons in a year. The results showed that Gammaproteobacteria and unassigned Actinobacteria were the most dominant bacterial communities, while the most dominant fungal communities were Dothideomycetes, unassigned Fungi, and Sodariomycetes. The bacterial community diversity in roots was higher than that in aerial tissues, and root communities had higher diversity in summer and autumn. In contrast, the fungal community diversity was higher in aerial tissues comparing to roots, and the highest diversity was in spring. Season was a determinant factor in the microbial community composition in the roots but not in the aerial tissues. RaupCrick index suggested that the bacterial communities were mainly shaped by stochastic processes. Our research investigated the community traits and members with temporal persistency. For example, bacterial taxa Afipia, Delftia, Stenotrophomonas, Xanthomonadaceae_B_OTU_211, and fungal taxa Neocamarosporium F_OTU_388, F_OTU_404, F_OTU_445, and unassigned Fungi F_OTU_704, F_OTU_767 showed higher frequencies than predicted in all the four seasons tested with neutral community model. The networks of co-occurrence associations presented in two or more seasons were visualized which suggested potential time-continuous core modules in most communities. In addition, the community dynamics and persistency also showed different patterns by radiation levels. Our findings would enhance our understanding of the microbial community assembly under environmental stress, and be promising to improve the development of integrated concept of core microbiome in future.


2021 ◽  
Author(s):  
Caterina Agrimonti ◽  
Giovanna Visoli ◽  
Graziano Ferrari ◽  
Anna Maria Sanangelantoni

Abstract The bacterial and archaeal communities of two biogas producing plants (P1 and P2), associated with a 999 kW cogeneration unit, both located in North Italy, were analyzed at start up and fully operating phases, by means of various molecular approaches: i) Automated Ribosomal Intergenic Spacer Analysis; ii) cloning and sequencing of PCR amplicons of archaeal genes 16Srrna and mcrA; iii) 16S rDNA high throughput next generation sequencing. P1 and P2 use the same technology and both were fed with cattle manure and corn silage. During the study of P1 also the post digestor (fed with pig manure) was analyzed. The aim of this research was to characterize the bacterial and archaeal community in two very similar plants to profile the core microbiome. The results of this analysis highlighted that the two plants (producing comparable quantities of volatile fatty acids, biogas, and energy) differed in anerobic microbiota (Bacteria and Archaea). Notably the methanogenic community of P1 was dominated by the strict acetoclastic Methanosaeta (Methanothrix) (up to 23.05%) and the unculturable Candidatus Methanofastidiosum (up to 32.70%), while P2 was dominated by the acetoclastic, but more substrate-versatile, Methanosarcina archaeal genus (49.19%). The data demonstrated that the performances of plants with identical design, in similar operating conditions, yielding comparable amount of biogas (average of 8662 m3 /day and 7916 m3/day respectively for P1 and P2), VFA (1643 mg/L and 1634 mg/L) and energy recovery (23.90-24 MWh/d) depends on the stabilization of an effective and functionally optimized methanogenic community rather than on the species composition


2021 ◽  
Author(s):  
Dong Hu ◽  
Liping Wang ◽  
Ran Zhao ◽  
Jie Zeng ◽  
Zongze Shao

2021 ◽  
Vol 12 ◽  
Author(s):  
Ahmed Elsheshtawy ◽  
Benjamin Gregory James Clokie ◽  
Amaya Albalat ◽  
Allan Beveridge ◽  
Ahmad Hamza ◽  
...  

The external mucosal surfaces of the fish harbor complex microbial communities, which may play pivotal roles in the physiological, metabolic, and immunological status of the host. Currently, little is known about the composition and role of these communities, whether they are species and/or tissue specific and whether they reflect their surrounding environment. Co-culture of fish, a common practice in semi-intensive aquaculture, where different fish species cohabit in the same contained environment, is an easily accessible and informative model toward understanding such interactions. This study provides the first in-depth characterization of gill and skin microbiomes in co-cultured Nile tilapia (Oreochromis niloticus) and grey mullet (Mugil capito) in semi-intensive pond systems in Egypt using 16S rRNA gene-based amplicon sequencing. Results showed that the microbiome composition of the external surfaces of both species and pond water was dominated by the following bacterial phyla: Proteobacteria, Fusobacteriota, Firmicutes, Planctomycetota, Verrucomicrobiota, Bacteroidota, and Actinobacteriota. However, water microbial communities had the highest abundance and richness and significantly diverged from the external microbiome of both species; thus, the external autochthonous communities are not a passive reflection of their allochthonous communities. The autochthonous bacterial communities of the skin were distinct from those of the gill in both species, indicating that the external microbiome is likely organ specific. However, gill autochthonous communities were clearly species specific, whereas skin communities showed higher commonalities between both species. Core microbiome analysis identified the presence of shared core taxa between both species and pond water in addition to organ-specific taxa within and between the core community of each species. These core taxa included possibly beneficial genera such as Uncultured Pirellulaceae, Exiguobacterium, and Cetobacterium and opportunistic potential pathogens such as Aeromonas, Plesiomonas, and Vibrio. This study provides the first in-depth mapping of bacterial communities in this semi-intensive system that in turn provides a foundation for further studies toward enhancing the health and welfare of these cultured fish and ensuring sustainability.


2021 ◽  
Author(s):  
Flavia Mansilla ◽  
Cecilia Ficoseco ◽  
María Miranda ◽  
Edoardo Puglisi ◽  
Maria Fatima Nader-Macias ◽  
...  

Abstract Modulation of animal gut microbiota is a prominent function of probiotics to improve the health and performance of livestock. In this study, a large-scale survey to evaluate the effect of lactic acid bacteria probiotics on shaping the fecal bacterial community structure of 126 feedlot cattle during three experimental periods of the fattening cycle (163 days) was conducted. A feedlot industry located in northwestern Argentina was enrolled with cattle fed mixed rations (forage and increasing grain diet). High-throughput sequencing (HTS) of 16S rDNA amplicons was applied to characterize the fecal microbiota and explore its modulation as affected by the administration of five probiotic groups and experimental administration periods. The microbial diversity of fecal samples was significantly affected (p < 0.05) by the administration period compared with probiotic group supplementation. The fecal microbiome of samples was dominated by the Firmicutes (72-98%) and Actinobacteria (0.8-27%) phyla, while a lower abundance of Bacteroidetes (0.08-4.2%) was present. At the family level, probiotics were able to modulate the fecal microbiota with a convergence of Clostridiaceae, Lachnospiraceae, Ruminococcaceae and Bifidobacteriaceae associated with health and growth benefits as core microbiome members. Metabolic functional prediction comparing experimental administration periods showed an enrichment of metabolic pathways related to complex plant-derived polysaccharide digestion as well as amino acids and derivatives during the first 40 days of probiotic supplementation. Genomic-based knowledge on the benefits of autochthonous probiotics on cattle gastrointestinal tract (GIT) microbiota composition and functions will contribute to their selection as antibiotic alternatives for the feedlot industry.


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