Comparing the Bacterial Community in the Gastrointestinal Tracts Between Growth-Retarded and Normal Yaks on the Qinghai–Tibetan Plateau

In ruminants, the bacterial community in the gastrointestinal tract (GIT) has an essential role in healthy growth. Examining the bacterial composition in the GIT between growth-retarded and normal yaks could improve our understanding of the role of microorganisms in yaks with growth retardation. In this study, eight male yaks with growth retardation were used as the growth-retarded yak (GRY) group, and another eight male growth normal yaks (GNYs) with the same breed and age were used as the GNY group. We compared the bacterial community in the rumen, duodenum, jejunum, ileum, cecum, and colon between GRY and GNY groups based on the 16S ribosomal RNA gene sequencing. Alpha-diversity revealed that the Shannon index in the duodenum and ileum of the GNY group was higher (P < 0.05) than that of the GRY group. However, the opposite trend was found in the jejunum and cecum. The principal coordinates analysis (PCoA) showed that the bacterial structure in all segments of GIT differed from each other between two groups. In the rumen, the relative abundances of Ruminococcaceae NK4A214 group, Ruminococcaceae UCG-014, and Treponema 2 were higher (P < 0.05) in the GNY group as compared with the GRY group. However, the Christensenellaceae R-7 group exhibited an opposite trend. In the jejunum, compared with the GNY group, the unclassified Chitinophagaceae was enriched significantly (P < 0.05) in the GRY group. However, the unclassified Peptostreptococcaceae, Christensenellaceae R-7 group, and Lachnospiraceae NK3A20 group were enriched (P < 0.05) in the GNY group. In the ileum, the relative abundances of the Rikenellaceae RC9 gut group and Prevotellaceae UCG-004 were higher (P < 0.05) in the GNY group than those in the GRY group. In the cecum, the GNY group showed a higher (P < 0.05) relative abundance of Prevotellaceae UCG-003 as compared with the GRY group. In the colon, the relative abundances of Treponema 2 and unclassified Lachnospiraceae were slightly higher (0.05 < P < 0.10) in the GNY group than those in the GRY group. Overall, these results improve our knowledge about the bacterial composition in the GIT of growth-retarded and normal yaks, and regulating the bacterial community may be an effective solution to promote the compensatory growth of GRYs.

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Calcified macroalgae and their bacterial community in relation to larval settlement and metamorphosis of reef-building coral Pocillopora damicornis

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa215 ◽

2020 ◽

Vol 97 (1) ◽

Author(s):

Fangfang Yang ◽

Jiahao Mo ◽

Zhangliang Wei ◽

Lijuan Long

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Bacterial Community Composition ◽

Larval Settlement ◽

Pocillopora Damicornis ◽

Principal Coordinates Analysis ◽

Principal Coordinates ◽

Coral Reef Ecosystems ◽

Settlement And Metamorphosis ◽

Invertebrate Larvae

ABSTRACT Calcified macroalgae play an important role in the settlement and metamorphosis of invertebrate larvae in coral reef ecosystems. However, little is known about the algal-associated bacterial communities and their effects on larval settlement. In this study, the responses of larvae of the coral Pocillopora damicornis to calcified algae (Porolithon onkodes, Halimeda cylindracea, Halimeda opuntia and Amphiroa fragilissima) were evaluated. The results revealed that Por. onkodes and H. cylindracea significantly enhanced the rates of settlement and metamorphosis, whereas fewer larvae settled on Am. fragilissima and H. opuntia. Amplicon pyrosequencing of the V3–V4 region of 16S rDNA was applied to investigate the relationship between algal bacterial community and larval settlement. Principal coordinates analysis demonstrated that the bacterial community composition of H. opuntia was more similar to that of Am. fragilissima, but clearly distinct from those of H. cylindracea and Por. onkodes. Furthermore, the relative abundances of bacteria were highly diverse among different algae. H. opuntia had higher percentages of Thalassobius, Pelagibius and SM1A02, whereas the abundances of Mycoplasma and Suttonella were significantly higher in H. cylindracea than other algae. Our results showed that larval settlement/metamorphosis was strongly correlated with the bacterial community composition and with the relative abundance of a few operational taxonomic units.

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Altitude influences microbial diversity and herbage fermentation in the rumen of yaks

BMC Microbiology ◽

10.1186/s12866-020-02054-5 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Qingshan Fan ◽

Metha Wanapat ◽

Tianhai Yan ◽

Fujiang Hou

Keyword(s):

Bacterial Community ◽

Microbial Diversity ◽

Volatile Fatty Acids ◽

Rumen Fluid ◽

Energy Requirement ◽

Tibet Plateau ◽

Limited Information ◽

Principal Coordinates Analysis ◽

Rumen Microbiota ◽

Principal Coordinates

Abstract Background Rumen microbiota in ruminants are vital for sustaining good rumen ecology, health, and productivity. Currently, limited information is available regarding the response of yaks (Bos grunniens) to fluctuating environments, especially the rumen microbiome. To address this, we investigated the diet, rumen bacterial community, and volatile fatty acids (VFA) of rumen fluid of yaks raised in the great Qinghai-Tibet plateau (QTP) at 2800 (low altitude, L), 3700 (middle altitude, M), and 4700 m (high altitude, H) above sea level. Results The results showed that despite a partial diet overlap, H yaks harbored higher fibrous fractious contents than the M and L grazing yaks. Bacteria including Christensenellaceae_R-7_group, Ruminococcus_1, Romboutsia, Alloprevotella, Eubacterium coprostanoligenes, Clostridium, Streptococcus, and Treponema were found to be enriched in the rumen of yaks grazing at H. They also showed higher rumen microbial diversity and total VFA concentrations than those shown by yaks at M and L. Principal coordinates analysis (PCoA) on weighted UniFrac distances revealed that the bacterial community structure of rumen differed between the three altitudes. Moreover, Tax4fun metagenome estimation revealed that microbial genes associated with energy requirement and carbohydrate metabolic fate were overexpressed in the rumen microbiota of H yaks. Conclusions Collectively, our results revealed that H yaks had a stronger herbage fermenting ability via rumen microbial fermentation. Their enhanced ability of utilizing herbage may be partly owing to a microbiota adaptation for more energy requirements in the harsh H environment, such as lower temperature and the risk of hypoxia.

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Improved normalization of species count data in ecology by scaling with ranked subsampling (SRS): application to microbial communities

PeerJ ◽

10.7717/peerj.9593 ◽

2020 ◽

Vol 8 ◽

pp. e9593 ◽

Cited By ~ 1

Author(s):

Lukas Beule ◽

Petr Karlovsky

Keyword(s):

Population Structure ◽

Community Structure ◽

Species Composition ◽

Microbial Communities ◽

Count Data ◽

Alpha Diversity ◽

Shannon Index ◽

Current Standard ◽

Library Size ◽

Relative Abundances

Background Analysis of species count data in ecology often requires normalization to an identical sample size. Rarefying (random subsampling without replacement), which is the current standard method for normalization, has been widely criticized for its poor reproducibility and potential distortion of the community structure. In the context of microbiome count data, researchers explicitly advised against the use of rarefying. Here we introduce a normalization method for species count data called scaling with ranked subsampling (SRS) and demonstrate its suitability for the analysis of microbial communities. Methods SRS consists of two steps. In the scaling step, the counts for all species or operational taxonomic units (OTUs) are divided by a scaling factor chosen in such a way that the sum of scaled counts equals the selected total number of counts Cmin. The relative frequencies of all OTUs remain unchanged. In the subsequent ranked subsampling step, non-integer count values are converted into integers by an algorithm that minimizes subsampling error with regard to the population structure (relative frequencies of species or OTUs) while keeping the total number of counts equal Cmin. SRS and rarefying were compared by normalizing a test library representing a soil bacterial community. Common parameters of biodiversity and population structure (Shannon index H’, species richness, species composition, and relative abundances of OTUs) were determined for libraries normalized to different size by rarefying as well as SRS with 10,000 replications each. An implementation of SRS in R is available for download (https://doi.org/10.20387/BONARES-2657-1NP3). Results SRS showed greater reproducibility and preserved OTU frequencies and alpha diversity better than rarefying. The variance in Shannon diversity increased with the reduction of the library size after rarefying but remained zero for SRS. Relative abundances of OTUs strongly varied among libraries generated by rarefying, whereas libraries normalized by SRS showed only negligible variation. Bray–Curtis index of dissimilarity among replicates of the same library normalized by rarefying revealed a large variation in species composition, which reached complete dissimilarity (not a single OTU shared) among some libraries rarefied to a small size. The dissimilarity among replicated libraries normalized by SRS remained negligibly low at each library size. The variance in dissimilarity increased with the decreasing library size after rarefying, whereas it remained either zero or negligibly low after SRS. Conclusions Normalization of OTU or species counts by scaling with ranked subsampling preserves the original community structure by minimizing subsampling errors. We therefore propose SRS for the normalization of biological count data.

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Characterization and Analysis of the Skin Microbiota in Acne: Impact of Systemic Antibiotics

Journal of Clinical Medicine ◽

10.3390/jcm9010168 ◽

2020 ◽

Vol 9 (1) ◽

pp. 168 ◽

Cited By ~ 3

Author(s):

Seo-Yeon Park ◽

Hei Sung Kim ◽

Se Hoon Lee ◽

Sungjoo Kim

Keyword(s):

Bacterial Species ◽

Alpha Diversity ◽

Skin Microbiota ◽

Principal Coordinates Analysis ◽

Severe Acne ◽

Doxycycline Treatment ◽

Principal Coordinates ◽

Cutibacterium Acnes ◽

Before And After ◽

Systemic Antibiotics

Systemic antibiotics are extensively used to control moderate to severe acne. Hence, it is crucial to understand their impact on the skin microbiota, which is supposedly perturbed. The purpose of this study was to compare the makeup and diversity of the skin microbiota in acne patients before and after taking oral antibiotics. A longitudinal cohort study was performed on 20 participants with moderate to severe facial acne with no recent use of oral and topical antibiotics/retinoids. Patients were prescribed oral doxycycline, 100 mg, twice daily for six weeks. Skin areas on the cheek were sampled for 16S ribosomal RNA gene sequencing at baseline, and after six weeks of doxycycline treatment. Ten males and 10 females aged 11 to 44 years with a median Investigator’s Global Assessment score of 3 (moderate) were enrolled. At baseline, Cutibacterium acnes (formerly Propionibacterium acnes) was the most dominant species followed by Staphylococcus epidermidis. Acne severity showed a positive correlation with the abundance of Cutibacterium acnes. Across all subjects, antibiotic treatment reduced clinical acne grades and was associated with a 1.96-fold reduction in the relative abundance of Cutibacterium acnes (p = 0.01, 95% CI −22% to −3%). Marked changes were also identified in other bacterial species, such as Cutibacterium granulosum (formerly Propionibacterium granulosum), which increased by 4.46-fold (p = 0.02, 95% CI 0.004% to 0.9%) in the treated samples. In general, antibiotics administration was associated with an increase in bacterial diversity (alpha diversity). Principal coordinates analysis showed mild clustering of samples by patient (analysis of similarity, R = 0.135, p = 0.04) whereas there was scant clustering with treatment (ANOSIM, R = 0.005; p = 0.29). In conclusion, we found individuals with acne to have a unique microbial signature. Acne treatment with systemic antibiotics was associated with changes in the composition and diversity of skin microbiota, especially Cutibacterium acnes, which correlates with acne severity. Our study provides insight into the skin microbiota in acne and how it is modulated by systemic antibiotics.

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Variations in the Compositions of Soil Bacterial and Fungal Communities Due to Microhabitat Effects Induced by Simulated Nitrogen Deposition of a Bamboo Forest in Wetland

Forests ◽

10.3390/f10121098 ◽

2019 ◽

Vol 10 (12) ◽

pp. 1098 ◽

Cited By ~ 1

Author(s):

Weicheng Li ◽

Haiyan Sheng ◽

Desy Ekawati ◽

Yueping Jiang ◽

Huimin Yang

Keyword(s):

Nitrogen Deposition ◽

Soil Ph ◽

Solid Phase ◽

Wetland Management ◽

Alpha Diversity ◽

Principal Coordinates Analysis ◽

Linear Discriminant ◽

Fungal Abundance ◽

Principal Coordinates ◽

Bacteria And Fungi

Although numerous studies have been published on nitrogen (N) deposition, little is known about its impact on microbial communities in wetland forests. Here, we used simulated nitrogen deposition (SND) to analyze the importance of differences in soil microhabitats in promoting the diversity of soil bacteria and fungi. We compared various levels of SND (control (CK), low N (N30), medium N (N60), and high N (N90)) and found that these were associated with changes in soil microhabitats. Additionally, SND affected soil pH, clay and sand content of the soil, and specific surface area (SSA). Bacteria and fungi responded differently to increased SND levels. The alpha diversity of bacteria decreased with an increased SND level, while fungal abundance, diversity, and community evenness reached their maximum values at the N60 threshold. Principal coordinates analysis (PCoA), nonparametric multivariate analysis of variance (PERMANOVA), and linear discriminant analysis (LDA) coupled with effect size measurements (LefSe) also confirmed that the bacterial composition was different at N90 compared to other levels of SND while that of fungi was different at N60. A higher discriminant level (LDA score ≥4) may be a valuable index of selecting indicator microbial clades sensitive to SND for wetland management. Further, an increased pH was associated with a greater abundance of bacteria and fungi. In addition, the volume contents of clay and SSA were negatively correlated with bacteria but fungi are associated with soil specific gravity (SSG). Overall, in a neutral soil pH environment, pH fluctuation is the main influencing factor in terms of bacterial and fungal abundance and diversity. The diversity of fungi is more dependent on the type and relative content of solid phase components in soil than that of bacteria, implying the presence of species-specific niches for bacteria and fungi. These results demonstrate that changes in SND can induce short-term microbial and microhabitat changes.

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Microbial Diversity in Tobacco Rhizosphere Soil at Different Growth Stages

Journal of Biobased Materials and Bioenergy ◽

10.1166/jbmb.2021.2102 ◽

2021 ◽

Vol 15 (5) ◽

pp. 606-614

Author(s):

Yanan Ruan ◽

Shengguang Xu ◽

Zuoxin Tang ◽

Xiaolin Liu ◽

Qirui Zhang ◽

...

Keyword(s):

Bacterial Community ◽

Microbial Diversity ◽

Rhizosphere Soil ◽

Principal Component ◽

Alpha Diversity ◽

Illumina Miseq ◽

Shannon Index ◽

Growth Stages ◽

Soil Microbial Diversity ◽

Different Growth Stages

Rhizosphere microorganisms are the main participants of material transformation and energy cycle in soil. To further explore its composition and variation, the tobacco rhizosphere soil were sequenced by Illumina MiSeq, the microbial community at different growth stages were analyzed and compared. The analysis of Alpha diversity showed that, the Chao1 index, Shannon index of bacteria and Chao1 index of fungi in rhizosphere soil were the highest in tobacco budding stage, while the peak of Shannon index of fungi appeared in tobacco material stage. Principal component analysis (PCA) further showed that at different growth stages, Proteobacteria was the dominant, followed by Actinobacteria, Acidobacteria and Gemmatimonadetes for bacterials; Ascomycota was the dominant, followed by Zygomycota and Basidiomycota for fungi. Under field conditions, the microbial abundance changed with the growth of tobacco, and the microbial diversity reached the peak at budding stage. The bacterial community and abundance between budding and mature stages was highly similar, while the bacterial community in vigorous growth stage is quite different. The similarity of fungal community in budding stage was very low, compared with the other stages; while in other stages was high. This study provides a theoretical basis for further understanding the relationship between tobacco rhizosphere soil microbial diversity and variation, tobacco growth and soil diseases.

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Genetic Diversity of Remaining Populations of Mangaba (Hancornia speciosa Gomes) in Restingas of Brazil

Journal of Agricultural Science ◽

10.5539/jas.v9n2p46 ◽

2017 ◽

Vol 9 (2) ◽

pp. 46 ◽

Cited By ~ 1

Author(s):

Ana Veruska Cruz da Silva ◽

Julie Anne Espíndola Amorim ◽

Marília Freitas de Vasconcelos Melo ◽

Ana Da Silva Ledo ◽

Allivia Rouse Carregosa Rabbani

Keyword(s):

Genetic Diversity ◽

Genetic Relationships ◽

Issr Markers ◽

Shannon Index ◽

Conservation Strategies ◽

Principal Coordinates Analysis ◽

Fruit Species ◽

Principal Coordinates ◽

Hancornia Speciosa ◽

Brazilian Northeast

Mangaba (Hancornia speciosa Gomes) is a fruit species that is native to Brazil, and has social, economic and cultural importance. Knowledge of the genetic relationships between the remaining populations is essential in order to promote conservation strategies for these genetic resources. In the present study, it was evaluated the genetic diversity of 35 individuals from three remaining restingas areas in the states of Ceará (Iguape and Cascavel) and Pernambuco (Tamandaré), located in the Brazilian Northeast. Nine ISSR primers were used to determine the genetic variability. Sixty-one fully polymorphic fragments (100%) were generated. The largest (10) and smallest (5) number of fragments were obtained with the primers HB14 and HB12, respectively. The Shannon index (I = 0.40), the genetic diversity (H = 0.30), and the percentage of polymorphic loci (%P = 73.77%) were also estimated. Both the methods of UPGMA and the Principal Coordinates Analysis (PCoA) clustered individuals according to their place of origin. Genetic divergence was greater within population (64%) than between them (36%). This may indicate a strong genetic structure, i.e., the gene flow rate between populations is low, favoring inbreeding. ISSR markers were efficient for the analysis of genetic diversity, for the identification of clusters, and for the estimation of the genetic distance between and within populations.

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Characterization and Analysis of the Skin Microbiota in Rosacea: Impact of Systemic Antibiotics

Journal of Clinical Medicine ◽

10.3390/jcm9010185 ◽

2020 ◽

Vol 9 (1) ◽

pp. 185 ◽

Cited By ~ 5

Author(s):

Yu Ri Woo ◽

Se Hoon Lee ◽

Sang Hyun Cho ◽

Jeong Deuk Lee ◽

Hei Sung Kim

Keyword(s):

Relative Abundance ◽

Alpha Diversity ◽

Age Group ◽

Skin Microbiota ◽

Principal Coordinates Analysis ◽

Doxycycline Treatment ◽

Principal Coordinates ◽

Cutibacterium Acnes ◽

Before And After ◽

Systemic Antibiotics

Systemic antibiotics are extensively used to control the papules and pustules of rosacea. Hence, it is crucial to understand their impact on the rosacea skin microbiota which is thought to be perturbed. The purpose of this study was to compare the makeup and diversity of the skin microbiota in rosacea before and after taking oral antibiotics. We also compared the skin microbiota at baseline according to age and rosacea severity. A longitudinal cohort study was performed on 12 rosacea patients with papules/pustules and no recent use of oral and topical antimicrobials/retinoids. Patients were prescribed oral doxycycline, 100 mg, twice daily for six weeks. Skin areas on the cheek and nose were sampled for 16S ribosomal RNA gene sequencing at baseline, and after six weeks of doxycycline treatment. Eleven females and one male aged 20–79 (median 51) with a median Investigator’s Global Assessment score of 3 (moderate) were enrolled. At baseline, Staphylococcus epidermidis was the most dominant species followed by Cutibacterium acnes (formerly Propionibacterium acnes). In the 60 Over-age group, the prevalence of Cutibacterium acnes was lower than that of the 60 & Under-age group. Rosacea severity increased with age and was associated with a decrease in the relative abundance of Cutibacterium acnes and an increase of Snodgrassella alvi. Across all subjects, antibiotic treatment reduced clinical rosacea grades and was associated with an increase in the relative abundance of Weissella confusa (P = 0.008, 95% CI 0.13% to 0.61%). Bacterial diversity (alpha diversity) was not significantly altered by antibiotics treatment. Principal coordinates analysis showed mild clustering of samples by patient (ANOSIM, Analysis of Similarity, R = 0.119, P = 0.16) and scant clustering with treatment (ANOSIM, R = 0.002; P = 0.5). In conclusion, we believe that rosacea has a unique age-dependent characteristic (i.e., severity). Although we were not able to pinpoint a causative microbiota, our study provides a glimpse into the skin microbiota in rosacea and its modulation by systemic antibiotics.

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Cyprus Sausages’ Bacterial Community Identification Through Metataxonomic Sequencing: Evaluation of the Impact of Different DNA Extraction Protocols on the Sausages’ Microbial Diversity Representation

Frontiers in Microbiology ◽

10.3389/fmicb.2021.662957 ◽

2021 ◽

Vol 12 ◽

Author(s):

Eleni Kamilari ◽

Marina Efthymiou ◽

Dimitrios A. Anagnostopoulos ◽

Dimitrios Tsaltas

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

Dna Extraction ◽

Bacterial Community Composition ◽

Alpha Diversity ◽

Rrna Gene ◽

Metagenomic Sequencing ◽

Additional Tool ◽

Principal Coordinates ◽

The Impact

Cyprus traditional sausages from the Troodos mountainous region of Pitsilia gained the protected geographical indication (PGI) designation from the European Committee (EU 2020/C 203/06). Still, we lack authentication protocols for the distinction of “Pitsilia” from industrially produced Cyprus sausages. Microbial activity is an essential contributor to traditional sausages’ sensorial characteristics, but whether the microbial patterns might be associated with the area of production is unclear. In the present research, we applied high-throughput sequencing (HTS) to provide a linkage between the area of production and Cyprus sausages’ bacterial diversity. To strengthen our findings, we used three different DNA extraction commercial kits: (i) the DNeasy PowerFood Microbial Kit (QIAGEN); (ii) the NucleoSpin Food Kit (MACHEREY-NAGEL); and (iii) the blackPREP Food DNA I Kit (Analytik Jena), in which we applied three different microbial cell wall lysis modifications. The modifications included heat treatment, bead beating, and enzymatic treatment. Results regarding metagenomic sequencing were evaluated in terms of number of reads, alpha diversity indexes, and taxonomic composition. The efficacy of each method of DNA isolation was assessed quantitatively based on the extracted DNA yield and the obtained copy number of (a) the 16S rRNA gene, (b) the internal transcribed spacer (ITS) region, and (c) three Gram-positive bacteria that belong to the genera Latilactobacillus (formerly Lactobacillus), Bacillus, and Enterococcus via absolute quantification using qPCR. Compared with some examined industrial sausages, Pitsilia sausages had significantly higher bacterial alpha diversity (Shannon and Simpson indexes). Principal coordinates analysis separated the total bacterial community composition (beta diversity) of the three Pitsilia sausages from the industrial sausages, with the exception of one industrial sausage produced in Pitsilia, according to the manufacturer. Although the eight sausages shared the abundant bacterial taxa based on 16S rDNA HTS, we observed differences associated with bacterial diversity representation and specific genera. The findings indicate that the microbial communities may be used as an additional tool for identifying of the authenticity of Cypriot sausages.

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Temporal Patterns of Bacterial and Viral Communities during Algae Blooms of a Reservoir in Macau

Toxins ◽

10.3390/toxins13120894 ◽

2021 ◽

Vol 13 (12) ◽

pp. 894

Author(s):

Dini Hu ◽

John P. Giesy ◽

Min Guo ◽

Wai Kin Ung ◽

Yijun Kong ◽

...

Keyword(s):

16S Rrna ◽

Alpha Diversity ◽

Diversity Indices ◽

Viral Metagenomics ◽

Principal Coordinates Analysis ◽

Algae Blooms ◽

Principal Coordinates ◽

Viral Communities ◽

Insight Into ◽

Generation Sequencing

Compositions of microbial communities associated with blooms of algae in a storage reservoir in Macau, China were investigated between 2013 and 2016. Algae were enumerated by visible light microscopy. Profiles of organisms in water were examined by 16S rRNA sequences and viral metagenomics, based on next generation sequencing. Results of 16S rRNA sequencing indicated that majority of the identified organisms were bacteria closely related to Proteobacteria, Cyanobacteria, Verrucomicrobia, Bacteroidetes, and Actinobacteria. Metagenomics sequences demonstrated that the dominant virus was Phycodnavirus, accounting for 70% of the total population. Patterns of relative numbers of bacteria in the microbial community and their temporal changes were determined through alpha diversity indices, principal coordinates analysis (PCoA), relative abundance, and visualized by Venn diagrams. Ways in which the bacterial and viral communities are influenced by various water-related variables were elucidated based on redundancy analysis (RDA). Relationships of the relative numbers of bacteria with trophic status in a reservoir used for drinking water in Macau, provided insight into associations of Phycodnavirus and Proteobacteria with changes in blooms of algae.

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