16S rRNA Gene Research Articles

Pseudohoeflea coraliihabitans sp. nov., a poly-β-hydroxybutyrate-producing, halotolerant bacterium isolated from coral sediment in the Dapeng peninsula (Guangdong, China).

A Gram-stain-negative, strictly aerobic, motile, flagellated, rod-shaped, halotolerant, and poly-β-hydroxyalkanoate-producing bacterium, designated DP4N28-3T, was isolated from offshore sediment surrounding hard coral in the Dapeng peninsula (Guangdong, PR China). Growth occurred at 15-35 °C (optimal at 30 °C), pH 6.0-9.5 (optimal at 6.0-7.0), and 0.0-30.0 % NaCl concentration (w/v, optimal at 0.0-2.0 %), showing halotolerance. Phylogeny based on 16S rRNA gene sequences, five housekeeping genes, and genome sequences identified Pseudohoeflea suaedae DSM 23348T (98.1 %, 16S rRNA gene sequence similarity) as the most related species to strain DP4N28-3T. Average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values between strain DP4N28-3T and P. suaedae DSM 23348T were all below the threshold of species demarcation. Major phenotypic differences were the flagella type and the limited sources of single carbon utilization by strain DP4N28-3T, which only included acetic acid, acetoacetic acid, d-glucuronic acid, and glucuronamide. Strain DP4N28-3T harboured the class I poly-β-hydroxyalkanoate synthase gene (phaC) and produced poly-β-hydroxybutyrate. The fatty acids were summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c, 49.4 %) and C16 : 0 (13.4 %). The major cellular polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, and sulfoquinovosyl diacylglycerol. The respiratory quinone was Q-10. The results of the phylogenetic, genomic, phenotypic, and chemotaxonomic analysis indicated that the isolated strain represents the type strain of a novel species. Based on these results, strain DP4N28-3T (=MCCC 1K05639T=KCTC 82803T) is proposed as the type strain of the novel species Pseudohoeflea coraliihabitans sp. nov.

Combined effects of polyvinyl chloride or polypropylene microplastics with cadmium on the intestine of zebrafish at environmentally relevant concentrations

Cadmium (Cd) is a common additive in polyvinyl chloride (PVC) and polypropylene (PP) plastics. Aquatic organisms were inevitably co-exposed to PVC/PP microplastics (MPs) and Cd, but their combined toxicity is still unknown. In this study, adult zebrafish were exposed to 200 μg/L MPs (PVC or PP) and 10 μg/L Cd alone or in combination for 28 days to investigate their toxicity and mechanisms. Results showed that combined exposure with PVC/PP enhanced the Cd accumulation in the zebrafish intestine. Subsequently, toxicology analyses showed that both PVC and PP possessed synergistic toxicity with Cd, manifested by the exfoliation and necrosis of intestinal epithelial cells, and increased levels of interleukin-1β (IL-1β), superoxide dismutase (SOD) and malondialdehyde (MDA). PP exhibited a stronger synergistic effect than PVC. Integration of non-targeted metabolomics and 16S rRNA gene sequencing revealed that combined exposure to PVC and Cd induced intestine toxicity mainly through bile acid (BA) biosynthesis, fructose (Fru) and mannose (Man) metabolism, and pentose phosphate pathway (PPP). The combined exposure of PP and Cd induced toxicity through the arginine (Arg) and glutathione (GSH) metabolisms. Meanwhile, combined exposure of PVC/PP and Cd increased the abundance of intestinal Proteobacteria and pathogen Vibrio, and decreased the abundance of Gemmobacter. These changes indrectly promoted the synergistic toxicity of PVC/PP and Cd through metabolites, such as indole-3-pyruvate (IPyA), chenodeoxycholic acid (CDCA), and cholic acid (CA). These findings highlighted that more attention should be paid to the toxicity of chemicals at environmentally relevant concentrations, particularly those co-existing with MPs.

Isolation and characterization of a novel bacterium that promotes the degradation of poly(glycolic acid) by its extracellular esterase under thermophilic conditions

Poly(glycolic acid) (PGA) is widely utilized in the shale oil and gas industry owing to its biodegradable nature, as well as superior mechanical and barrier properties. However, PGA degradability is limited by environmental conditions such as temperature and pH, and using acids to optimize the degradation can have adverse environmental impact. Thus, it is essential to identify methods that can effectively promote the degradation of PGA under mild conditions, such as microbial degradation. In the present study, strain DB14, a bacterium that promotes PGA degradation, was isolated from drain water of a steam pipeline. Sequence analysis of the 16S rRNA gene of the bacterium revealed that it is mostly closely related to Geobacillus icigianus; however, it also differed from Geobacillus icigianus in several physiological properties. To investigate PGA degradation by strain DB14, a PGA film and disc were incubated with the strain. The residual weight of the PGA film (thickness: 170 μm) significantly reduced after incubation, whereas the decrease in the thickness of the PGA disc (thickness: 3 mm) was relatively small. The penetration of water, the bacterium, and the extracellular enzymes into the interior from the reaction-erosion front of the PGA disc may be inhibited by the high barrier performance of PGA. Strain DB14 was also found to change the pH of the surrounding environment to approximately 8–9. To investigate the effect of pH on PGA degradability, degradation tests with crude extracellular enzymes derived from strain DB14 were conducted in various buffers. The results showed that the degradation activity was highest at pH 8, which implied that DB14 efficiently maximized the hydrolytic capacity of its enzyme for degrading PGA. Thus, this study provides a basis for developing environmentally friendly technologies that can promote the degradation of PGA molding articles, especially those used in wellbores for oil and gas recovery.

Flourishing in Darkness: Protist Communities of Water Sites in Shulgan-Tash Cave (Southern Urals, Russia)

Karst caves, formed by the erosion of soluble carbonate rocks, provide unique ecosystems characterized by stable temperatures and high humidity. These conditions support diverse microbial communities, including wall microbial fouling, aquatic biofilms, and planktonic communities. This study discloses the taxonomic diversity of protists in aquatic biotopes of Shulgan-Tash Cave, a culturally significant site and popular tourist destination, by 18S rRNA gene metabarcoding. Our findings reveal the rich protist communities in the cave’s aquatic biotopes, with the highest diversity observed in Blue Lake at the cave entrance. In contrast, Distant Lake in the depth of the cave was inhabited by specific communities of plankton, mats, and pool fingers, which exhibited lower richness and evenness, and were adapted to extreme conditions (cold, darkness, and limited nutrients). High-rank taxa including Opisthokonta, Stramenopiles, and Rhizaria dominated all biotopes, aligning with observations from other subterranean environments. Specific communities of biotopes inside the cave featured distinct dominant taxa: amoeboid stramenopile (Synchromophyceae) and flagellates (Choanoflagellatea and Sandona) in mats; flagellates (Choanoflagellatea, Bicoecaceae, Ancyromonadida) and amoeboid protists (Filasterea) in pool fingers; flagellates (Ochromonadales, Glissomonadida, Synchromophyceae), fungi-like protists (Peronosporomycetes), and fungi (Ustilaginomycotina) in plankton. The specificity of the communities was supported by LEfSe analysis, which revealed enriched or differentially abundant protist taxa in each type of biotope. The predominance of Choanoflagellatea in the communities of cave mats and pool fingers, as well as the predominance of Synchromophyceae in the cave mats, appears to be a unique feature of Shulgan-Tash Cave. The cold-tolerant yeast Malassezia recorded in other caves was present in both plankton and biofilm communities, suggesting its resilience to low temperatures. However, no potentially harmful fungi were detected, positioning this research as a baseline for future monitoring. Our results emphasize the need for ongoing surveillance and conservation efforts to protect the fragile ecosystems of Shulgan-Tash Cave from human-induced disturbances and microbial invasions.

Development of a highly specific LAMP assay for detection of Sarcocystis tenella and Sarcocystis gigantea in sheep.

Sarcocystis infection in sheep has caused significant economic losses in the livestock industry, and the genetic similarity among Sarcocystis species highlights the need for precise diagnostic methods in sheep. This study developed a loop-mediated isothermal amplification (LAMP) method targeting COX-1 and 28S rRNA genes to detect Sarcocystis tenella and Sarcocystis gigantea, respectively. The LAMP method exhibited high specificity, selectively amplifying target DNA sequences without cross-reactivity with closely related protozoa, such as Toxoplasma gondii and Neospora caninum. Detection limits were determined as 3 × 105 copies/L for S. tenella and 6 × 104 copies/L for S. gigantea, enabling sensitive identification of low-level infections. Comparative analysis with conventional PCR on sheep cardiac tissues demonstrated a higher LAMP detection rate (80.0% vs 66.7%). In conclusion, the LAMP method offers superior sensitivity to conventional PCR, allows visual confirmation of results, and provides a rapid diagnostic tool for identifying S. tenella and S. gigantea infection in sheep. However, due to the limitation of sample availability, we were unable to assess all Sarcocystis species that use sheep as intermediate hosts, which warrants further research.

Trematode metacercariae parasitic in the estuarine crustacean Cyathura muromiensis Nunomura, 1974 (Peracarida: Isopoda: Anthuroidea)

This is the first report of trematodes parasitic in the estuarine isopod crustacean Cyathura muromiensis, and the fourth report from anthuroid isopods worldwide. From 52 of 54 host individuals collected qualitatively on the tidal flat of the Muromi River estuary, Fukuoka, Japan, 389 cysts of metacercariae were extracted (sample prevalence = 96.3 %). Host individuals contained from one to 71 metacercarial cysts. The range in cyst diameter was 172.3–252.1 μm, and the distribution of cyst sizes contained only one component. Cysts occurred in pereonites 2–7 and the pleon of the host, but not in the head, pereonite 1, or telson. There was no correlation between the number of cysts and host sex or size. Sequences of the nuclear “ITS1 region,” from the 3´ region of 18S rRNA to the 5´ region of internal transcribed spacer I gene (ITS1), from five cysts ranging in size from nearly the lowest diameter to the greatest diameter in our sample showed p-distances of 0.0–0.2 %, suggesting that all cysts obtained were conspecific. A phylogenetic reconstruction based on nuclear 28S rRNA gene sequences showed that the trematode belongs in the genus Microphallus. The definitive host of our trematode species is likely a bird, since the definitive hosts of microphallids are chiefly birds, and birds are known to prey on Cyathura isopods.

Bacillus cereus containing nheA, hblC and cytk enterotoxin genes is associated with acute childhood gastroenteritis in Nigeria.

Bacillus cereus is rarely implicated when diarrheal cases in children are diagnosed in developing countries due to the lack of molecular methods to identify its enterotoxigenic genes. We report that out of 62 enterobacteria isolated from 70 stool samples collected from children hospitalized at the Mile 4 Hospital, Ebonyi State, Nigeria, 24 isolates were identified as B. cereus based on 16SrRNA gene sequence. The enterotoxins genes nheA and cytK2 were detected in 23 out of the 24 isolates, while hblC was detected in 19 isolates. B. cereus may be responsible for greater number of yearly incidences of acute childhood gastroenteritis in Nigeria.

Ticks and tick-borne pathogens in selected abattoirs and a slaughter slab in Kumasi, Ghana.

Ticks are vectors of pathogens that affect the health of animals and humans. With the constant trade of livestock across borders, there is the risk of new tick species invasion accompanied by the spread of infectious tick-borne pathogens. This study sought to determine the diversity of tick species within abattoirs and a slaughter slab as well as identify the pathogens carried by these ticks. The ticks were collected from slaughtered cattle, identified and screened for pathogens using PCR and sequencing. A total of 371 ticks were collected from slaughtered cattle across the three sampling sites: Kumasi abattoir (288, 77.63%), Akwatia Line slaughter slab (52, 14.02%) and Suame abattoir (31, 8.35%). The predominant species was Amblyomma variegatum (85.44%) with Rhipicephalus sanguineus (s.l.) (0.27%) as the least occurring species. Total nucleic acid from the tick pools was screened for pathogens based on the nucleoprotein gene region in the S segment of the Crimean-Congo haemorrhagic fever virus (CCHFV) genome, the 295-bp fragment of the transposase gene of the Coxiella burnetii IS1111a element, the 560bp segment of the ssrRNA gene of Babesia and Theileria, the 345bp fragment of the Ehrlichia genus 16SrRNA gene and the rOmpA gene (OmpA) of Rickettsia. From the 52 tick pools screened, 40 (76.92%) were found positive for pathogen DNA. The pathogens identified were Rickettsia africae (69.23%), Rickettsia aeschlimannii (7.69%), C. burnetii (5.77%), uncultured Ehrlichia sp. (5.77%), Candidatus Midichloria mitochondrii (3.85%) and CCHFV (3.85%). A significant association was observed among A. variegatum, Hyalomma rufipes, Hyalomma truncatum and occurring tick-borne pathogens R. africae, R. aeschlimannii and uncultured Ehrlichia sp. (p<0.001). The findings show the occurrence of zoonotic pathogens, suggesting an increased risk of infections among the abattoir workers. There is a need to adopt control measures within the abattoirs to prevent pathogen spread.

Potassium-induced κ-carrageenan helices resist degradation by gut microbiota in an in vitro model

Higher-order structures hierarchy of κ-carrageenan in the presence of potassium was reported. Yet, the destiny of κ-carrageenan in higher-order structures in the colon and their impacts on the gut microbiota community remains to be revealed. This study aims to investigate the fermentation behaviors and trace the structural change of higher-order structures of κ-carrageenan during in vitro fermentation. Herein, κ-carrageenan gels were induced in the presence of 10, 40, and 70 mmol/L potassium ions, and a structural-hierarchical transition from secondary to quaternary structures was observed using an AFM and TEM. Results from GPC-MALLS, TLC, IEC, and GC indicated that Single helices were partially fermented by fecal microbiota, while supercoiled helices (tertiary structures) and intertwined helices networks (quaternary structures) were hardly fermented. Tracing the structural change of higher-order κ-carrageenan suggested that the single helices were partially deformed, as shown by the 60% reduction of single helices width, while supercoiled helices were more resistant to fermentation compared to single helices. The super-strands networks were hardly fermented as their width distribution center had been sustained at around 90 nm from 12 to 48 h. In addition, the 16S rRNA gene (V3-V4) amplicon sequencing results indicated that Bifidobacterium longum showed a positive correlation to the structural hierarchy (R = 0.734, p < 0.01). Together, the higher-order structures hierarchy of κ-carrageenan can resist degradation by human gut microbiota.

Clinicopathologic Characterization of Invasive Fungal Intestinal Infections in Pediatric Patients.

Invasive fungal intestinal infections are rare in pediatric patients with limited studies reported to date. Retrospective study of invasive intestinal fungal infections in pediatric patients. For fungal specification, 18S rRNA gene PCR was performed using formalin-fixed paraffin-embedded tissues. A total of 19 cases from 18 patients were included (13 males, 72%) with a median age of 20 days (8 days-14 years). About 13 patients (72%) presented within 67 days of birth and 11 patients (61%) were premature and 14 patients (78%) had a significant medical history. The most common location was the jejunum/ileum (56%) followed by the right colon and terminal ileum (22%). In 10 patients, the fungal elements were seen in the mucosa with 3 extending into the submucosa, and only 3 patients showed full-thickness involvement. Tissue necrosis and angioinvasion were seen in 13 (72%) and 8 (44%) patients, respectively. Morphologically, organisms consistent with Candida spp. were seen in 17 patients and with a mucoraceous mold in 1 patient. A 18S rRNA gene sequencing performed in 18 cases identified Candida dubliniensis in 16 cases and Candida spp. in 2 cases. During the study follow-up period, 56% of the patients died. In our experience, most cases were due to Candida spp. and predominantly in premature infants and associated with poor outcomes.

Molecular diversity of green-colored microbial mats from hot springs of northern Japan.

We acquired and analyzed metagenome and 16S/18S rRNA gene amplicon data of green-colored microbial mats from two hot springs within the Onikobe geothermal region (Miyagi Prefecture, Japan). The two collection sites-Tamago and Warabi-were in proximity and had the same temperature (40°C), but the Tamago site was connected to a nearby stream, whereas the Warabi site was isolated. Both the amplicon and metagenome data suggest the bacterial, especially cyanobacterial, dominance of the mats; other abundant groups include Chloroflexota, Pseudomonadota, Bacteroidota/Chlorobiota, and Deinococcota. At finer resolution, however, the taxonomic composition entirely differed between the mats. A total of 5 and 21 abundant bacterial 16S rRNA gene OTUs were identified for Tamago and Warabi, respectively; of these, 12 are putative chlorophyll- or rhodopsin-based phototrophs. The presence of phylogenetically diverse microbial eukaryotes was noted, with ciliates and amoebozoans being the most abundant eukaryote groups for Tamago and Warabi, respectively. Fifteen metagenome-assembled genomes (MAGs) were obtained, represented by 13 bacteria, one ciliate (mitochondrion), and one giant virus. A total of 15 novel taxa, including a new deeply branching Chlorobiota species, is noted from the amplicon and MAG data, highlighting the importance of environmental sequencing in uncovering hidden microorganisms.

Association of Oral Microbiome with Periodontal Disease Progression: A Longitudinal Study

Periodontal disease, a prevalent oral health condition, is characterized by the inflammation and destruction of the supporting tissues around the teeth and poses significant challenges to global public health. Objectives: To examine the association between the oral microbiome and periodontal disease progression in a Pakistani population. Methods: A total of 350 patients aged ≥ 18 years, diagnosed with periodontal disease, were registered from August 2023 to February 2024. Participants were evaluated for periodontal health indicators, including probing depth and clinical attachment loss, and their oral microbiome profiles were analyzed using high-throughput sequencing of the 16S rRNA gene. Machine learning algorithms, including Random Forest and Support Vector Machines, were applied to predict disease progression based on microbial profiles. Results: Porphyromonas gingivalis and Tannerella forsythia were strongly associated with greater probing depths and clinical attachment loss (β = 0.45, p &lt; 0.01), indicating their role in disease progression. Conversely, Streptococcus and Lactobacillus were linked to reduced disease severity (β = -0.30, p &lt; 0.05). The oral microbiome exhibited high diversity, with Firmicutes (35%), Bacteroidetes (25%), Proteobacteria (20%), and Actinobacteria (15%) being the predominant species. The Random Forest model predicted disease progression with 85% accuracy (Area under the curve (AUC) = 0.87), emphasizing the predictive value of microbial profiles. Conclusions: It was concluded that the study confirms a strong link between specific oral microbiota and periodontal disease progression, emphasizing the importance of microbial analysis in predicting and managing periodontal health.

Isolation and Characterization of Bacteriocin Producing Levilactobacillus brevis Strain ABRIINW-K from Buffalo Dung

Bacteriocins are proteins secreted by many species of bacteria to inhibit other bacteria, thus eliminating competitors to gain resources. Bacteria from the Lactobacillus group are known for their applications as probiotics and food preservatives. They have earned a reputation for producing substances that inhibit the growth of other microorganisms, which include organic acids, diacetyl, and bacteriocins. Produced by the ribosomes, bacteriocins are cationic proteins that inhibit other bacteria coexisting within a shared ecological habitat. Due to their potential uses in a variety of applications large-scale production of Bacteriocins would be necessary. The study aimed to identify and characterize Lactobacillus bacteria that produce potent bacteriocins and to analyze the antimicrobial activity and stability of the isolated bacteriocin under various physical and biochemical conditions. A total of 50 samples including buffalo dung, cheese, and rhizospheric region of plants were screened to isolate 8 Lactobacillus Li-1, Li-2, Li-3, Li-4, Li-5, Li-6, Li-7, and Li-8, confirmed by gram staining and other biochemical tests. The cell free supernatant from the Li-3 strain showed higher inhibition of Escherichia coli and Staphylococcus aureus, as compared to the other isolated strains. Li-3 strain was further identified as Levilactobacillus brevis strain ABRIINW-K by 16S rRNA gene sequencing. The bacteriocin isolated from this strain is a thermostable peptide (~6kDa), which is characteristic of class II bacteriocins, with potent antibacterial activity against Lactobacillus rhamnosus, Escherichia coli, and Salmonella enterica.

Aloe arborescens supplementation in drying-off dairy cows: influence on rumen, rectum and milk microbiomes

BackgroundIn the context of the RABOLA project, which aimed to identify operational practices that lead to the reduction of antibiotic use in dairy cattle farming, lyophilised Aloe arborescens was administered orally to cows during the dry-off and peripartum periods. In this specific paper we wanted to examine whether oral administration of Aloe arborescens, in combination with the topical application of a teat sealant could exert an effect on the microbial populations of three cow microbiomes (rumen, milk, rectum), between dry-off and peripartum. Dry-off and peripartum are critical physiological phases of the cow’s life, where both the mammary gland and the gastrointestinal tract undergo dramatic modifications, hence the relevance of evaluating the effects of dietary treatments.MethodsThirty multiparous dairy cows were randomly allocated to three groups: Control (antibiotic treatment and internal teat sealant), Sealant (only internal teat sealant) and Aloe (internal teat sealant and Aloe arborescens homogenate administered orally). For 16S rRNA gene sequencing, rumen, rectum and milk samples were collected, not synchronously, at the most critical timepoints around dry-off and calving, considering the physiological activity of each biological site.ResultsThe rumen microbiome was predominantly characterized by Bacteroidetes and Firmicutes followed by Proteobacteria, while the rectum exhibited a prevalence of Firmicutes and Bacteroidetes. The milk microbiome mainly comprised Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. Alistipes spp., Ruminococcaceae UCG-10 group, Prevotellaceae UCG-001 group, and Bacteroides spp., involved in cellulose and hemicellulose degradation, enhancement of energy metabolism, and peptide breakdown, showed increment in the rectum microbiome with Aloe supplementation. The rectum microbiome in the Aloe group exhibited a significant increase in the Firmicutes to Bacteroidetes ratio and alpha-diversity at seven days after dry-off period. Beta-diversity showed a significant separation between treatments for the rectum and milk microbiomes. Aloe supplementation seemed to enrich milk microbial composition, whereas the Sealant group showed greater diversity compared to the Control group, albeit this included an increase in microorganisms frequently associated with mastitis.ConclusionsAloe arborescens administration during the dry-off period did not demonstrate any observable impact on the microbial composition of the rumen, a finding further supported by volatilome analysis. Instead, the oral Aloe supplementation at dry-off appears to significantly influence the composition of the dairy cow rectum and milk microbiomes in the following lactation.

High-solid digestion – A comparison of completely stirred and plug-flow reactor systems

High-solid digestion (HSD) for biogas production is a resource-efficient and sustainable method to treat organic wastes with high total solids content and obtain renewable energy and an organic fertiliser, using a lower dilution rate than in the more common wet digestion process. This study examined the effect of reactor type on the performance of an HSD process, comparing plug-flow (PFR) type reactors developed for continuous HSD processes, and completely stirred-tank reactors (CSTRs) commonly used for wet digestion. The HSD process was operated in thermophilic conditions (52 °C), with a mixture of household waste, garden waste and agricultural residues (total solids content 27–28 %). The PFRs showed slightly better performance, with higher specific methane production and nitrogen mineralisation than the CSTRs, while the reduction of volatile solids was the same in both reactor types. Results from 16S rRNA gene sequencing showed a significant difference in the microbial population, potentially related to large differences in stirring speed between the reactor types (1 rpm in PFRs and 70–150 rpm in CSTRs, respectively). The bacterial community was dominated by the genus Defluviitoga in the PFRs and order MBA03 in the CSTRs. For the archaeal community, there was a predominance of the genus Methanoculleus in the PFRs, and of the genera Methanosarcina and Methanothermobacter in the CSTRs. Despite these shifts in microbiology, the results showed that stable digestion of substrates with high total solids content can be achieved in both reactor types, indicating flexibility in the choice of technique for HSD processes.

Diversity and structure of prokaryotic assemblages in a thermally stratified tropical lake

The structure and diversity of prokaryotic assemblages in inland waters are strongly related to their habitat. Yet, there is a lack of integrative studies surveying them in different compartments in tropical lakes. This study estimated the diversity and composition of prokaryotic assemblages in sediments, microbialites, and water column in the tropical warm monomictic Lake Alchichica and identified the most representative phylotypes while thermally stratified. The 16S rRNA gene survey showed a distinctive prokaryotic assemblage for each compartment, with 60–78 % of the phylotypes being unique to each one. Sediments accounted for the major prokaryotic diversity in the lake, with chemoorganotrophic bacteria and sulphate reducers as major biogeochemical components. Microbialites showed a high abundance of oxygenic and anoxygenic phototrophs, as well as organotrophs. The prokaryoplancton in the water column was mainly composed of picocyanobacteria and Flavobacteria in the epilimnion, shifting to a high diversity of anaerobic microorganisms in the hypolimnion. These water column assemblages were significantly correlated to pH, ORP, DO, and nutrient concentration. This study shows an integral view of the prokaryotic assemblages in a deep tropical lake related to physicochemical characteristics, from their diversity to their biogeochemical implications, suggesting the role of lake sediments as a possible microbial seed bank.

Unde venis? Bacterial resistance from environmental reservoirs to lettuce: tracking microbiome and resistome over a growth period.

Fresh produce is suggested to contribute highly to shaping the gut resistome. We investigated the impact of pig manure and irrigation water quality on microbiome and resistome of field-grown lettuce over an entire growth period. Lettuce was grown under four regimes, combining soil amendment with manure (with/without) with sprinkler irrigation using river water with an upstream wastewater input, disinfected by UV (with/without). Lettuce leaves, soil, and water samples were collected weekly and analyzed by bacterial cultivation, 16S rRNA gene amplicon sequencing, and shotgun metagenomics from total community DNA. Cultivation yielded only few clinically relevant antibiotic-resistant bacteria (ARB), but numbers of ARB on lettuce increased over time, while no treatment-dependent changes were observed. Microbiome analysis confirmed a temporal trend. Antibiotic resistance genes (ARGs) unique to lettuce and water included multidrug and β-lactam ARGs, whereas lettuce and soil uniquely shared mainly glycopeptide and tetracycline ARGs. Surface water carried clinically relevant ARB (e.g. ESBL-producing Escherichia coli or Serratia fonticola) without affecting the overall lettuce resistome significantly. Resistance markers including biocide and metal resistance were increased in lettuce grown with manure, especially young lettuce (increased soil contact). Overall, while all investigated environments had their share as sources of the lettuce resistome, manure was the main source especially on young plants. We therefore suggest minimizing soil-vegetable contact to minimize resistance markers on fresh produce.

Associations of Neonatal Dairy Calf Faecal Microbiota with Inflammatory Markers and Future Performance.

After birth, the immune system is challenged by numerous elements of the extrauterine environment, reflected in fluctuations of inflammatory markers. The concentrations of these markers in the first month of life are associated with the future performance of dairy youngstock. It is thought that bacterial genera colonizing the calf intestinal tract can cause inflammation and thus affect their host's performance via immunomodulation. This study explored how the faecal microbiota of newborn dairy calves were related to inflammatory markers during the first three weeks of life, and if the abundance of specific genera was associated with first-lactation performance. Ninety-five female Holstein calves were studied. Once a week, serum and faecal samples were collected, serum concentrations of serum amyloid A, haptoglobin, tumour necrosis factor-α, and interleukin-6 were measured, and faecal microbiota composition was examined by 16S rRNA gene amplicon sequencing. Faecal Gallibacterium abundance in the first week of age and Collinsella abundance in the second week were negatively associated with inflammatory response as well as with calving-conception interval. Peptostreptococcus abundance in the second week of life was positively associated with inflammatory response and calving-conception interval, and negatively with average daily weight gain. In the third week, Dorea abundance was positively, Bilophila abundance was negatively associated with inflammatory response, and both genera were negatively associated with age at first calving. These bacterial genera may be able to influence the inflammatory response and through this, possibly the future performance of the dairy heifer. Deciphering such microbiota-host interactions can help improve calf management to benefit production and welfare.

Potential Trimethylamine (TMA)-Producing Bacteria in patients with chronic kidney disease undergoing hemodialysis.

Trimethylamine (TMA), produced by gut microbiota, is the precursor of trimethylamine-N-oxide (TMAO), a uremic toxin that accumulates in patients with chronic kidney disease (CKD). Elevated TMAO plasma levels are associated with cardiovascular complications and CKD progression. To evaluate the association between gut microbiota composition and TMAO plasma levels in CKD patients undergoing hemodialysis (HD). This is a cross-sectional study with 25 patients evaluated (60% female, 53 (18) years, body mass index (BMI) 25.8 (6.75)Kg/m2). They were divided into two groups according to their TMAO plasma levels: normal (≤ 7.4μM) and high (> 7.4μM). Uremic toxins such as indoxyl sulfate (IS), p-cresyl sulfate (pCS), and indol acetic acid (IAA) were measured with RP-HPLC, and TMAO plasma levels were quantified using LC-MS/MS. Fecal DNA was extracted with a commercial kit, PCR amplified the V4 region of the 16S rRNA gene, and short-read sequencing was performed on the Illumina platform. Dietary intake, anthropometric measurements, and inflammation markers were also evaluated. Nrf2, NF-κB, IL-1β, and NLRP3 mRNA expressions were measured from peripheral blood mononuclear cells (PBMC) using quantitative real-time polymerase chain reaction (qPCR). There were significant positive correlations between TMAO and plasma levels of pCS, NLPR3 inflammasome mRNA expression, serum phosphorus levels, and negative correlations with dietary lipid intake. The group with TMAO > 7.4μM showed an increase in the microbiome abundance of Saccharibacteria (genus incertae sedis), Colidextribacter, Dorea, and Staphylococci genera, and a decrease in abundance in the genera Lachnospira, Lactobacilli, and Victivallis. TMAO plasma level was positively correlated with the abundance of bacteria of the genera Colidextribacter and Helicobacter and was negatively correlated with Sphingomanos, Lachnospira, Streptomyces, and Bacillus genera. Saccharibacteria (genus incertae sedis), Colidextribacter, Dorea, and Staphylococci genera showed higher abundance in patients with high TMAO levels. In addition, we observed that elevated plasma TMAO levels are associated with inflammation markers, dietary lipid intake, and serum phosphorus levels in patients undergoing HD.

16S rRNA gene sequencing of microbiota from the preen oil and cloaca of chipping sparrows (Spizella passerina).

We present the results of 16S rRNA gene amplicon sequencing of the microbiota from preen oil and the cloaca of chipping sparrows (Spizella passerina) collected near Mountain Lake Biological Station in Pembroke, VA.