Changes In Bacterial Populations Research Articles

복분자 와인을 첨가한 요구르트의 품질 특성

복분자 와인을 첨가한 요구르트의 배양 중 변화는 모든 시험구에서 pH는 배양 시간이 지날수록 낮아지는 변화를 보였으며, 적정산도와 점도는 점차적으로 증가하는 경향을 보였다. 유산균수의 변화는 모든 시험구에서 시간이 지날수록 유산균수가 증가하는 경향을 나타 내었으며 5.0% 첨가구에서 가장 많은 유산균 수를 나타내었다. 저장 중 변화는 모든 시험구에서 저장 기간이 길어질수록 pH값이 점차 낮아졌으며 시간이 경과할수록 첨가구보다는 대조구에서 더 낮은 pH값을 나타내었다. 적정산도의 변화는 5.0%, 3.0% 첨가구가 1.0% 첨가구와 대조구보다 낮은 적정산도값을 나타내었고 점도의 변화는 0일에는 첨가구보다 대조구의 점성이 높았으나 6일 이후에는 대조구가 모든 첨가구의 점성보다 낮았다. 유산균수의 변화는 저장기간 내내 대조구보다 첨가구에서 높은 유산균수를 나타내었으며, 복분자 와인을 첨가한 요구르트의 알코올 함량, 안토시아닌 색소 함량과 TPA함량은 복분자 와인의 첨가량이 많을수록 수치도 높게 나타났다. 관능검사 결과, 첨가량이 증가할수록 색감과 조직성에서 선호도가 증가하는 것을 나타내었다. 복분자 와인을 첨가한 요구르트 제조 시험에서 5.0% 첨가구가 pH, 유산균 수, 점도와 안토시아닌 색소 회수 함량, total phenolic 함량과 관능평가에서 가장 우수한 성적을 보였다. This study was conducted to evaluate the quality characteristics of yoghurt added with 1.0%, 3.0% and 5.0% Bokbunja wine (BW) during the preparation of yoghurt. Changes of lactic acid bacterial population, pH, and total titratable acidity (TA) were monitored during the fermentation and storage of yoghurt. The pH was decreased in all the treatments, also TA and viscosity were gradually increased during the fermentation. The viscosity of yoghurt added with 5.0% BW was higher than another group. The sensory test, total phenolic acid and the anthocyanins content of the yoghurt were measured. The results of this analysis showed that higher amounts of total TA, viscosity, lactic acid bacterial population, total phenolic acid content and sensory test were observed in the yoghurt supplemented with the BW than those of yoghurt not supplemented with the BW. Sensory scores in yoghurt added 5.0% BW were significantly higher than the other groups in taste. When the BW yoghurt was kept at <TEX>$4^{\circ}C$</TEX> for 12 d, its quality-keeping properties were relatively good. The combined results of this study suggest that yoghurt supplementing with BW produces additional nutrients while maintaining the flavor and quality.

Evaluating changes in cellulolytic bacterial population to explain methane emissions from air-dried and composted manure treated rice paddy soils

Compost application recorded ~20% reduction in methane (CH4) emission during rice cultivation as compared to air-dried manure treatment. The objective of this study was to evaluate the dependence of methanogens on cellulolytic bacteria (CB) to produce CH4 in organic-amended rice paddy soils. The presence of more decomposable organic C in manure was probably the key factor for higher CH4 emission from manure-treated soils as compared to compost application. Manure application facilitated anaerobic CB abundance in rice paddy soils, and that in turn increased concentrations of dissolved organic C compounds like carbohydrates in soil. Soluble organic C compounds are converted into acetate and/or carbon dioxide, which act as initial energy source for methanogens. Therefore, it could be concluded that CB positively influenced methanogen activity and methanogenesis and stabilized organic substrates like compost are more rational treatment to mitigate CH4 emission from rice paddy soil than cattle manure application.

Intestinal bacterial community structure differs between healthy and inflamed intestines in Atlantic salmon (Salmo salar L.)

Atlantic salmon ( Salmo salar L.) fed soybean meal (SBM) are known to develop SBM-induced enteritis with atrophy of intestinal folds and inflammation in the lamina propria. In this study, intestinal contents of mid (MI) and distal intestine (DI) were collected from 12 fish fed one of the following diets for 80 days: a fish meal (FM) diet and SBM diet. Polymerase chain reaction denaturing gradient gel electrophoresis analysis of 16S ribosomal ribonucleic acid gene was used to evaluate whether changes in bacterial population were associated with healthy and inflamed intestines. Fish fed the same diet were mainly clustered together in both MI and DI. The diversity indices were strongly reduced by the SBM diet in DI, as shown by both richness and Shannon–Weaver indices. The SBM diet gave a higher relative abundance of Firmicutes bacteria than the FM diet in the DI. The most dominant species were Lactococcus lactis subsp. lactis , Weissella confusa , and Photobacterium phosphoreum . To conclude, the intestinal bacterial population was highly affected by dietary conditions and might play a role in the development of SBM-induced enteritis. • Bacterial population of healthy and inflamed intestines was evaluated. • The use PCR-DGGE allows screening of changes in the intestinal bacterial community. • The bacterial community differs between healthy and inflames intestines. • SBM diet gave increased relative abundance of Firmicutes bacteria in the distal intestine. • Intestinal bacteria could play a role in the SBM-induced enteritis.

Drastic changes in aquatic bacterial populations from the Cuatro Cienegas Basin (Mexico) in response to long-term environmental stress

Understanding the changes of aquatic microbial community composition in response to changes in temperature and ultraviolet irradiation is relevant for predicting biogeochemical modifications in the functioning of natural microbial communities under global climate change scenarios. Herein we investigate shifts in the bacterioplankton composition in response to long-term changes in temperature and UV radiation. For this purpose, 15 mesocosms were seeded with composite aquatic microbial communities from natural pools within the Cuatro Cienegas Basin (Mexican Chihuahuan desert) and were subject to different temperatures and UV conditions. 16S rRNA gene clone libraries were obtained from water samples at the mid-point (4 months) and the end of the experiment (8 months). An increase in bacterial diversity over time was found in the treatment of constant temperature and UV protection, which suggests that stable environments promote the establishment of complex and diverse bacterial community. Drastic changes in the phylogenetic bacterioplankton composition and structure were observed in response to fluctuating temperature and increasing UV radiation and temperature. Fluctuating temperature induced the largest decrease of bacterial richness during the experiment, indicating that frequent temperature changes drive the reduction in abundance of several species, most notably autotrophs. The long-term impact of these environmental stresses reduced diversity and selected for generalist aquatic bacterial populations, such as Porphyrobacter. These changes at the community level occur at an ecological time scale, suggesting that under global warming scenarios cascade effects on the food web are possible if the microbial diversity is modified.

Impact of subacute ruminal acidosis (SARA) adaptation on rumen microbiota in dairy cattle using pyrosequencing

The objective of this study was to evaluate the changes in bacterial populations in the rumen of dairy cattle following adaptation to subacute ruminal acidosis (SARA) using 16S rRNA gene pyrosequencing. Rumen contents were collected from four cattle adapted to either a 40% (control diet, COD) or 70% (SARA induction diet, SAID) concentrate feeds. DNA was extracted from each of the samples. Bacterial 16S rRNA genes of ruminal DNA extracts were PCR amplified with 2 bar coded primer sets and sequenced by 454 pyrosequencing. At a high taxonomic level, the percentage of Proteobacteria and Bacteroidetes were reduced by SAID feeding, whereas Firmicutes and Actinobacteria were more abundant in the SAID than in the COD group. At the genus level, as compared with the COD group, the abundances of Prevotella, Treponema, Anaeroplasma, Papillibacter, Acinetobacter and unclassified populations including unclassified Lentisphaerae, and unclassified bacteria were lower (P < 0.05), while the percentages of Ruminococcus, Atopobium, unclassified Clostridiales and Bifidobacterium were increased (P < 0.05) in the SAID group. Feeding of SAID reduced (P < 0.001) the diversity of the rumen microbial community. Taken together, our findings provide a comprehensive picture of current knowledge of the community structure of the rumen bacterial ecosystem during SARA, and enhance our understanding about the ruminal microbial ecology that may be useful in the prevention of ruminal acidosis.

Actinomyces Ruminicola G10 - The Rumen Bacterium Recovered from Glycerol Enriched Cultivation Media

Abstract Gradual increasing of glycerol concentration up to 10% using sheep ruminal fluid as an inoculum for in vitro cultivation was accompanied by significant changes in bacterial population as documented by DGGE analysis. The resulting bacterial consortium was composed of three dominant bacteria with Actinomyces related bacterium to be predominant. Upon cultivation on media with glycerol as a sole carbon source a single bacterium was cultivated from this consortium. Isolate G10 was found to be anaerobic, Gram-positive rod-shaped bacterium. Phylogenetic analysis based on 16S rRNA gene sequences showed that G10 isolate is related to the Actinomyces ruminicola species (97.7% of similarity). The role of rumen actinobacteria is largely unknown and their participation in glycerol utilization (tolerance) has not been described yet. The G10 bacterium and related consortium could be possibly used to improve glycerol tolerance and uptake by ruminants

Use of Pyrosequencing to Characterize the Microbiota in the Ileum of Goats Fed with Increasing Proportion of Dietary Grain

This study evaluated the effects of an increasing proportion of dietary grain on changes in bacterial populations in the goat ileum. Nine ruminally fistulated, castrated male goats were assigned to three diets in a completely randomized design. Goats were fed three different dietary treatments containing different proportions of corn grain (0, 25, and 50%). The pH of the ileal contents and rumen fluid (P=0.015) linearly decreased (P<0.001), and the acetate, propionate, butyrate, and total volatile fatty acid in ileal contents increased (P<0.05) with increases in dietary corn, and similar results were also observed in rumen fluid. The barcoded DNA pyrosequencing method was used to reveal 8 phyla, 70 genera, and 1,693 16S operational taxonomic units (OTUs). At the genus level, the proportions of Acetitomaculum, Enterococcus, Atopobium, unclassified Coriobacteriaceae, and unclassified Planctomycetaceae were linearly decreased (P<0.05) with increases in corn grain. At the species level, high grain feeding linearly decreased the percentage of OTU8686 (unclassified Bacteria) (P=0.004). To the best of our knowledge, this is the first study using barcoded DNA pyrosequencing method to survey the ileal microbiome of goats and the results suggest that increasing levels of dietary corn change the composition of the ileal bacterial community. These findings provide previously unknown information about the ileal microbiota of goats and a new understanding of the ileal microbial ecology, which may be useful in modulating the gut microbiome.

Analysis of fermentation selectivity of purified galacto-oligosaccharides by in vitro human faecal fermentation

The in vitro fermentation of several purified galacto-oligosaccharides (GOS), specifically the trisaccharides 4'-galactosyl-lactose and 6'-galactosyl-lactose and a mixture of the disaccharides 6-galactobiose and allolactose, was carried out. The bifidogenic effect of GOS at 1% (w/v) was studied in a pH-controlled batch culture fermentation system inoculated with healthy adult human faeces. Results were compared with those obtained with a commercial GOS mixture (Bimuno-GOS). Changes in bacterial populations measured through fluorescence in situ hybridization and short-chain fatty acid (SCFA) production were determined. Bifidobacteria increased after 10-h fermentation for all the GOS substrates, but the changes were only statistically significant (P<0.05) for the mixture of disaccharides and Bimuno-GOS. Acetic acid, whose formation is consistent with bifidobacteria metabolism, was the major SCFA synthesized. The acetate concentration at 10 h was similar with all the substrates (45-50 mM) and significantly higher than the observed for formic, propionic and butyric acids. All the purified GOS could be considered bifidogenic under the assayed conditions, displaying a selectivity index in the range 2.1-3.0, which was slightly lower than the determined for the commercial mixture Bimuno-GOS.

Involvement of dietary salt in shaping bacterial communities in European sea bass (Dicentrarchus labrax)

Bacteria associated with the digestive tract of multicellular organisms have been shown to play a major role in their hosts' functioning. In fish, it has been proposed that food fermentation occurs inside the pyloric ceca, pouch like organs found in their digestive tract. However, this notion remains controversial. Furthermore, changes in pyloric cecal bacterial populations under different diets have yet to be demonstrated in fish. In this study, we explore the changes occurring in the bacterial community residing in the pyloric ceca of carnivorous fish fed different diets, which were shown to induce different growth rates. Our results revealed that different diets do indeed induce distinct bacterial compositions within the pyloric ceca. We found that, when salt was added to a low fish meal diet, the bacterial changes were accompanied by a significant enhancement in weight gain, hinting at a possible involvement of the bacterial community in energy harvest.

Radiant energy under vacuum (REV) technology: A novel approach for producing probiotic enriched apple snacks

The feasibility of vacuum impregnation in combination with air drying+radiant energy vacuum (REV) drying to produce shelf stable probiotic enriched apple slices was evaluated. The shelf life of the products was monitored at 25 and 4°C. The results demonstrated that bacterial stability at 25°C depended on the dehydration techniques; with the longest shelf life in air drying +REV drying followed by freeze drying and air drying. Storage at 4°C showed no significant changes in bacterial population up to 180days in all samples. Sensory properties of the air drying +REV and freeze dried apple slices remained above the acceptable level for 30days at 25°C and 180days at 4°C. The results also revealed that dried apple slices were able to provide prominent protection to the cells in acidic gastric juice.

HCl-Extractable Metal Profiles Correlate with Bacterial Population Shifts in Metal-Impacted Anoxic Coastal Sediment from the Wet/Dry Tropics

Metal impacted, anoxic sediments from five sites at a coastal location in the wet/dry tropics of Australia were sampled during both wet and dry seasons. Metal concentrations in total sediment and porewater, and in potentially bioavailable and bioaccessible fractions, were measured. Pyrosequencing was used to sequence bacterial DNA extracted from the sediment, and the sequence data was used to generate community profiles at each sample site. Changes in bacterial populations between sites reflected changes in the concentrations of 7 metals/metalloids (Al, V, Mo, Ga, Zn, Cd, As), and best correlated with the HCl-extractable fraction of metals. Bacterial community structure was also related to physicochemical factors, such as redox potential and organic carbon. Despite a strong sulphide gradient across the transect, acid-volatile sulphide was not significantly correlated to bacterial community structure. We conclude that the bioaccessible fraction of metals to bacteria is partly comprised of particulates, and porewater alone is not a sufficient model for potential metal impact. [Supplementary materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the two supplementary tables.]

Chocolate, gut microbiota, and human health

Chocolate, gut microbiota, and human health

In Vitro Fermentation of Lactulose-Derived Oligosaccharides by Mixed Fecal Microbiota

Fermentation properties of oligosaccharides derived from lactulose (OsLu) and lactose (GOS) have been assessed in pH-controlled anaerobic batch cultures using lactulose and Vivinal-GOS as reference carbohydrates. Changes in gut bacterial populations and their metabolic activities were monitored over 24 h by fluorescent in situ hybridization (FISH) and by measurement of short-chain fatty acid (SCFA) production. Lactulose-derived oligosaccharides were selectively fermented by Bifidobacterium and lactic acid bacterial populations producing higher SCFA concentrations compared to GOS. The highest total SCFA production was from Vivinal-GOS > lactulose > OsLu > GOS. Longer incubation periods produced a selective fermentation of OsLu when they were used as a carbon source reaching the highest selective index scores. The new oligosaccharides may constitute a good alternative to lactulose, and they could belong to a new generation of prebiotics to be used as a functional ingredient for improving the composition of gut microflora.

Microbiological quality of raw donkey milk from Campania Region

Microbiological quality of raw milk from eight healthy donkeys reared in Campania Region was investigated. A total of 152 samples were analyzed in order to evaluate the milk safety status trough monitoring mesophilic total bacterial count (TBC) at 32°C and 20°C, psychrophilic TBC at 5°C, Enterobacteriaceae, Salmonella spp., Listeria monocytogenes, Staphylococcus aureus and somatic cell count (SCC). The ranges for mesophilic bacteria at 32°C, 20°C and psy- chrophilic bacteria at 5°C were, respectively, 2.80–4.00 Log CFU/mL, 2.84–3.92 Log CFU/mL and 1.27–2.12 Log CFU/ml. Enterobacteriaceae showed a load ranging between 0.68–1.93 Log CFU/mL. No pathogenic bacteria were isolated. Estimated SCC values were always under 50.000 cells/mL. Additionally quantitative changes of bacterial population in raw bulk milk during eight storing days at 8°C and 3°C, were evaluated. Firstly, fresh bulk milk was contaminated by bacteria with a mean TBC at 32°C and 20°C of 2.71 Log CFU/mL and 2.64 Log CFU/mL, respectively, whereas TBC at 5°C and Enterobacteriaceae were not detected. After eight days of storage at 8°C, TBC at 32°C, 20°C and Enterobacteriaceae increased by three Log and TBC at 5°C by five Log. On the other side, after eight days of storage at 3°C no gradual Log increase was detected. Our results showed that donkey milk could be a good healthy ingredient for feeding where good hygienic procedures are applied and storage is kept at temperature lower than 3°C.

Microbiota benefits after inulin and partially hydrolized guar gum supplementation: a randomized clinical trial in constipated women.

Prebiotics positively affect gut microbiota composition, thus improving gut function. These properties may be useful for the treatment of constipation. This study assessed the tolerance and effectiveness of a prebiotic inulin/partially hydrolyzed guar gum mixture (I-PHGG) for the treatment of constipation in females, as well as its influence on the composition of intestinal microbiota and production of short chain fatty acids. Our study enrolled 60 constipated female health worker volunteers. Participants reported less than 3 bowel movements per week. Volunteers were randomized to treatment with prebiotic or placebo. Treatment consisted of 3 weeks supplementation with 15 g/d IPHGG (fiber group) or maltodextrin (placebo group). Abdominal discomfort, flatulence, stool consistency, and bowel movements were evaluated by a recorded daily questionnaire and a weekly interview. Changes in fecal bacterial population and short chain fatty acids were assessed by real-time PCR and gas chromatography, respectively. There was an increased frequency of weekly bowel movements and patient satisfaction in both the fiber and placebo groups with no significant differences. Total Clostridium sp significantly decreased in the fiber group (p = 0.046) and increased in the placebo group (p = 0.047). There were no changes in fecal short chain fatty acid profile. Consumption of I-PHGG produced clinical results comparable to placebo in constipated females, but had additional protective effects on gut microbiota by decreasing the amount of pathological bacteria of the Clostridium genera.

Archaeal community composition affects the function of anaerobic co-digesters in response to organic overload

Microbial community diversity in two thermophilic laboratory-scale and three full-scale anaerobic co-digesters was analysed by genetic profiling based on PCR-amplified partial 16S rRNA genes. In parallel operated laboratory reactors a stepwise increase of the organic loading rate (OLR) resulted in a decrease of methane production and an accumulation of volatile fatty acids (VFAs). However, almost threefold different OLRs were necessary to inhibit the gas production in the reactors. During stable reactor performance, no significant differences in the bacterial community structures were detected, except for in the archaeal communities. Sequencing of archaeal PCR products revealed a dominance of the acetoclastic methanogen Methanosarcina thermophila, while hydrogenotrophic methanogens were of minor importance and differed additionally in their abundance between reactors. As a consequence of the perturbation, changes in bacterial and archaeal populations were observed. After organic overload, hydrogenotrophic methanogens (Methanospirillum hungatei and Methanoculleus receptaculi) became more dominant, especially in the reactor attributed by a higher OLR capacity. In addition, aggregates composed of mineral and organic layers formed during organic overload and indicated tight spatial relationships between minerals and microbial processes that may support de-acidification processes in over-acidified sludge.Comparative analyses of mesophilic stationary phase full-scale reactors additionally indicated a correlation between the diversity of methanogens and the VFA concentration combined with the methane yield. This study demonstrates that the coexistence of two types of methanogens, i.e. hydrogenotrophic and acetoclastic methanogens is necessary to respond successfully to perturbation and leads to stable process performance.

Bile Acid Is a Host Factor That Regulates the Composition of the Cecal Microbiota in Rats

Alterations in the gastrointestinal microbiota have been associated with metabolic diseases. However, little is known about host factors that induce changes in gastrointestinal bacterial populations. We investigated the role of bile acids in this process because of their strong antimicrobial activities, specifically the effects of cholic acid administration on the composition of the gut microbiota in a rat model. Rats were fed diets supplemented with different concentrations of cholic acid for 10 days. We used 16S ribosomal RNA gene clone library sequencing and fluorescence in situ hybridization to characterize the composition of the cecal microbiota of the different diet groups. Bile acids in feces, organic acids in cecal contents, and some blood parameters were also analyzed. Administration of cholic acid induced phylum-level alterations in the composition of the gut microbiota; Firmicutes predominated at the expense of Bacteroidetes. Cholic acid feeding simplified the composition of the microbiota, with outgrowth of several bacteria in the classes Clostridia and Erysipelotrichi. Externally administered cholic acid was efficiently transformed into deoxycholic acid by a bacterial 7α-dehydroxylation reaction. Serum levels of adiponectin decreased significantly in rats given the cholic acid diet. Cholic acid regulates the composition of gut microbiota in rats, inducing similar changes to those induced by high-fat diets. These findings improve our understanding of the relationship between metabolic diseases and the composition of the gastrointestinal microbiota.

Effect of glycation of bovine β-lactoglobulin with galactooligosaccharides on the growth of human faecal bacteria

The in vitro fermentation selectivity of purified galactooligosaccharides (GOS) after their conjugation with bovine β-lactoglobulin (β-LG) via the Maillard reaction and a subsequent simulated gastrointestinal digestion was evaluated. Changes in human faecal bacterial populations, lactic acid and short-chain fatty acids after 10 h and 24 h of fermentation of the digested β-LG:GOS conjugates revealed that this mixture of glycated peptides had a similar bifidogenic activity to the unconjugated GOS. These findings could open up new applications for Maillard reaction products in the functional foods field.

Marine microbial community response to inorganic and organic sediment amendments in laboratory mesocosms

Sediment amendments provide promising strategies of enhancing sequestration of heavy metals and degradation of organic contaminants. The impacts of sediment amendments for metal and organic remediation including apatite, organoclay (and apatite and organoclay in geotextile mats), acetate, and chitin on environmental microbial communities in overlying water and sediment profiles are reported here. These experiments were performed concurrent with an ecotoxicity evaluation (data submitted in companion paper) and X-ray absorption spectroscopy of zinc speciation post apatite amendments. X-ray absorption spectra showed that a modest modification of zinc speciation occurred in amended treatments. Significant changes in both bacterial cell densities and populations were observed in response to amendments of apatite+organoclay, chitin, and acetate. The enriched bacteria and breakdown of these amendments were likely attributed to water quality degradation (e.g. ammonia and dissolved oxygen). Molecular fingerprints of bacterial communities by denaturant gradient gel electrophoresis (DGGE) showed that distinct bacterial populations occurred in overlying waters from different amendments: apatite+organoclay led to the dominance of Gammaproteobacteria, acetate enriched Alphaproteobacteria, and chitin treatment led to a dominance of Bacteroidetes and Alphaproteobacteria. In amended sediments, Firmicutes, Bacteroidetes, and Deltaproteobacteria ( Desulfovibrio) were commonly found with chitin and apatite+chitin treatments. Finally, sulfate-reducing bacteria (e.g. Desulfovibrio) and metal-reducing bacteria were also recovered with most probable number (MPN) analyses in treatments with acetate, chitin, and apatite+chitin. These geochemically important bacteria were stimulated by amendments and may play critical functional roles in the metal and organic contaminant remediation process for future investigations of contaminated sediments.

Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset

BackgroundThe world's oceans are home to a diverse array of microbial life whose metabolic activity helps to drive the earth's biogeochemical cycles. Metagenomic analysis has revolutionized our access to these communities, providing a system-scale perspective of microbial community interactions. However, while metagenome sequencing can provide useful estimates of the relative change in abundance of specific genes and taxa between environments or over time, this does not investigate the relative changes in the production or consumption of different metabolites.ResultsWe propose a methodology, Predicted Relative Metabolic Turnover (PRMT) that defines and enables exploration of metabolite-space inferred from the metagenome. Our analysis of metagenomic data from a time-series study in the Western English Channel demonstrated considerable correlations between predicted relative metabolic turnover and seasonal changes in abundance of measured environmental parameters as well as with observed seasonal changes in bacterial population structure.ConclusionsThe PRMT method was successfully applied to metagenomic data to explore the Western English Channel microbial metabalome to generate specific, biologically testable hypotheses. Generated hypotheses linked organic phosphate utilization to Gammaproteobactaria, Plantcomycetes, and Betaproteobacteria, chitin degradation to Actinomycetes, and potential small molecule biosynthesis pathways for Lentisphaerae, Chlamydiae, and Crenarchaeota. The PRMT method can be applied as a general tool for the analysis of additional metagenomic or transcriptomic datasets.