Doing More with Less: A Comparison of 16S Hypervariable Regions in Search of Defining the Shrimp Microbiota

Whole-cell biocatalysis for phthalate esters biodegradation in wastewater by a saline soil bacteria SSB-consortium

Phthalic acid esters (PAE) are widely used as plasticizers and have been classified as ubiquitous environmental contaminants of primary concern. PAE have accumulated intensively in surface water, groundwater, and wastewaters; thus, PAE degradation is essential. In the present study, the ability of a saline soil bacteria (SSB)-consortium to degrade synthetic wastewater-phthalates with alkyl chains of different lengths, such as diethyl phthalate (DEP), di-n-butyl phthalate (DBP), benzyl butyl phthalate (BBP), and di (2-ethylhexyl) phthalate (DEHP) was characterized. A central composite design-response surface methodology was applied to optimize the degradation of each phthalate, where the independent variables were temperature (21-41 °C), pH (5.3-8.6) and PAE concentration (79.5-920.4 mg L-1), and Gas Chromatography-Mass Spectrometry was used to identify the metabolites generated during phthalate degradation. Optimal conditions were 31 °C, pH 7.0, and an initial PAE concentration of 500 mg L-1, where the SSB-consortium removed 84.9%, 98.47%, 99.09% and 98.25% of initial DEP, DBP, BBP, and DEHP, respectively, in 168h. A first-order kinetic model explained - the biodegradation progression, while the half-life of PAE degradation ranged from 12.8 to 29.8 h. Genera distribution of the SSB-consortium was determined by bacterial meta-taxonomic analysis. Serratia, Methylobacillus, Acrhomobacter, and Pseudomonas were the predominant genera; however, the type of phthalate directly affected their distribution. Scanning electron microscopy analysis showed that high concentrations (1000 mg L-1) of phthalates induced morphological alterations in the bacterial SSB-consortium. The metabolite profiling showed that DEP, DBP, BBP, and DEHP could be fully metabolized through the de-esterification and β-oxidation pathways. Therefore, the SSB-consortium can be considered a potential candidate for bioremediation of complex phthalate-contaminated water resources.

Low salinity stress increases the risk of Vibrio parahaemolyticus infection and gut microbiota dysbiosis in Pacific white shrimp

BACKGROUND

Extreme precipitation events often cause sudden drops in salinity, leading to disease outbreaks in shrimp aquaculture. Evidence suggests that environmental stress increases animal host susceptibility to pathogens. However, the mechanisms of how low salinity stress induces disease susceptibility remain poorly understood.

METHODS

We investigated the acute response of shrimp gut microbiota exposed to pathogens under low salinity stress. For comparison, shrimp were exposed to Vibrio infection under two salinity conditions: optimal salinity (Control group) and low salinity stress (Stress group). High throughput 16S rRNA sequencing and real-time PCR were employed to characterize the shrimp gut microbiota and quantify the severity level of Vibrio infection.

RESULTS

The results showed that low salinity stress increased Vibrio infection levels, reduced gut microbiota species richness, and perturbed microbial functions in the shrimp gut, leading to significant changes in lipopolysaccharide biosynthesis that promoted the growth of pathogens. Gut microbiota of the bacterial genera Candidatus Bacilliplasma, Cellvibrio, and Photobacterium were identified as biomarkers of the Stress group. The functions of the gut microbiota in the Stress group were primarily associated with cellular processes and the metabolism of lipid-related compounds.

CONCLUSIONS

Our findings reveal how environmental stress, particularly low salinity, increases shrimp susceptibility to Vibrio infection by affecting the gut microbiota. This highlights the importance of avoiding low salinity stress and promoting gut microbiota resilience to maintain the health of shrimp.

The effects of clays on bacterial community composition during arthropod decay

Fossilization, or the transition of an organism from the biosphere to the geosphere, is a complex mechanism involving numerous biological and geological variables. Bacteria are one of the most significant biotic players to decompose organic matter in natural environments, early on during fossilization. However, bacterial processes are difficult to characterize as many different abiotic conditions can influence bacterial efficiency in degrading tissues. One potentially important variable is the composition and nature of the sediment on which a carcass is deposited after death. We experimentally examined this by decaying the marine shrimp Palaemon varians underwater on three different clay sediments. Samples were then analyzed using 16S ribosomal RNA sequencing to identify the bacterial communities associated with each clay system. Results show that samples decaying on the surface of kaolinite have a lower bacterial diversity than those decaying on the surface of bentonite and montmorillonite, which could explain the limited decay of carcasses deposited on this clay. However, this is not the only role played by kaolinite, as a greater proportion of gram-negative over gram-positive bacteria is observed in this system. Gram-positive bacteria are generally thought to be more efficient at recycling complex polysaccharides such as those forming the body walls of arthropods. This is the first experimental evidence of sediments shaping an entire bacterial community. Such interaction between sediments and bacteria might have contributed to arthropods' exquisite preservation and prevalence in kaolinite-rich Lagerstätten of the Cambrian Explosion.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13358-024-00324-7.

Comparative analysis of growth and health of juvenile African catfish (Clarias gariepinus) fed with different starch diets

This study evaluated the effects of potato, wheat, rice, and corn starch on growth performance, blood parameters, digestive enzyme activity, antioxidative response, and gut microbiota of African catfish, Clarias gariepinus. A control diet (a commercial fish diet) and four different starch (potato, PO; wheat, WH; corn, CO; rice, RC) formulations were fed to African catfish with average weight of 10.5g (n = 30) for eight weeks. The experiment was conducted in triplicates. At the end of the feeding trial, the growth performance of African catfish fed with potato starch (PO) was significantly higher than other treatment groups. Furthermore, this group recorded significant and lowest feed conversion ratio (FCR) compared to other groups. Meanwhile, there were no significant differences in all tested hematological parameters and antioxidative response between the groups. Digestive enzyme activities in the fish intestines, including amylase, lipase, and protease, were significantly higher in African catfish fed with the PO diet. In addition, this group demonstrated substantially lower viscerosomatic index (VSI) and hepatosomatic index (HSI) than other groups, indicating that the fish has more meat on its body. The PO diet group also recorded significantly higher Akkermansia muciniphila, a good gut microbiota. Therefore, the PO diet potentially improves African catfish's growth performance and health status.

Acute Ammonia Causes Pathogenic Dysbiosis of Shrimp Gut Biofilms

Acute ammonia exposure has detrimental effects on shrimp, but the underlying mechanisms remain to be fully explored. In the present study, we investigated the impact of acute ammonia exposure on the gut microbiota of the white shrimp Litopenaeus vannamei and its association with shrimp mortality. Exposure to a lethal concentration of ammonia for 48 h resulted in increased mortality in L. vannamei, with severe damage to the hepatopancreas. Ammonia exposure led to a significant decrease in gut microbial diversity, along with the loss of beneficial bacterial taxa and the proliferation of pathogenic Vibrio strains. A phenotypic analysis revealed a transition from the dominance of aerobic to facultative anaerobic strains due to ammonia exposure. A functional analysis revealed that ammonia exposure led to an enrichment of genes related to biofilm formation, host colonization, and virulence pathogenicity. A species-level analysis and experiments suggest the key role of a Vibrio harveyi strain in causing shrimp disease and specificity under distinct environments. These findings provide new information on the mechanism of shrimp disease under environmental changes.

Shrimp microbiome and immune development in the early life stages

With its contribution to nutrition, development, and disease resistance, gut microbiome has been recognized as a crucial component of the animal's health and well-being. Microbiome in the gastrointestinal tract constantly interacts with the host animal's immune systems as part of the normal function of the intestines. Interactions between the microbiome and the immune system are complex and dynamic, with the microbiome shaping immune development and function. In contrast, the immune system modulates the composition and activity of the microbiome. In shrimp, as with all other aquatic animals, the interaction between the microbiome and the animals occurs at the early developmental stages. This early interaction is likely essential to the development of immune responses of the animal as well as many key physiological developments that further contribute to the health of shrimp. This review provides background knowledge on the early developmental stage of shrimp and its microbiome, examines the interaction between the microbiome and the immune system in the early life stage of shrimp, and discusses potential pitfalls and challenges associated with microbiome research. Understanding the interaction between the microbiome and shrimp immune system at this crucial developmental stage could have the potential to aid in the establishment of a healthy microbiome, improve shrimp survival, and provide ways to shape the microbiome with feed supplements or other strategies.

A metagenomic comparison of clearwater, probiotic, and Rapid BFTTM on Pacific whiteleg shrimp, Litopenaeus vannamei cultures

Biofloc technology improves water quality and promote the growth of beneficial bacteria community in shrimp culture. However, little is known about the bacteria community structure in both water and gut of cultured organisms. To address this, the current study characterised the metagenomes derived from water and shrimp intestine samples of novel Rapid BFTTM with probiotic and clearwater treatments using 16S V4 region and full length 16S sequencing. Bacteria diversity of water and intestine samples of Rapid BFTTM and probiotic treatments were similar. Based on the 16S V4 region, water samples of >20 μm biofloc had the highest abundance of amplicon sequence variant (ASV). However, based on full length 16S, no clear distinction in microbial diversity was observed between water samples and intestine samples. Proteobacteria was the most abundant taxon in all samples based on both 16S V4 and full length 16S sequences. Vibrio was among the highest genus based on 16S V4 region but only full length 16S was able to discern up to species level, with three Vibrios identified-V. harveyi, V. parahaemolyticus and V. vulnificus. Vibrio harveyi being the most abundant species in all treatments. Among water samples, biofloc water samples had the lowest abundance of all three Vibrios, with V. vulnificus was present only in bioflocs of <20 μm. Predicted functional profiles of treatments support the beneficial impacts of probiotic and biofloc inclusion into shrimp culture system. This study highlights the potential displacement of opportunistic pathogens by the usage of biofloc technology (Rapid BFTTM) in shrimp culture.

Microbial biomarker detection in shrimp larvae rearing water as putative bio-surveillance proxies in shrimp aquaculture

Background

Aquacultured animals are reared in water hosting various microorganisms with which they are in close relationships during their whole lifecycle as some of these microorganisms can be involved in their host's health or physiology. In aquaculture hatcheries, understanding the interactions existing between the natural seawater microbiota, the rearing water microbiota, the larval stage and the larval health status, may allow the establishment of microbial proxies to monitor the rearing ecosystems. Indeed, these proxies could help to define the optimal microbiota for shrimp larval development and could ultimately help microbial management.

Methods

In this context, we monitored the daily composition of the active microbiota of the rearing water in a hatchery of the Pacific blue shrimp Penaeus stylirostris. Two distinct rearing conditions were analyzed; one with antibiotics added to the rearing water and one without antibiotics. During this rearing, healthy larvae with a high survival rate and unhealthy larvae with a high mortality rate were observed. Using HiSeq sequencing of the V4 region of the 16S rRNA gene of the water microbiota, coupled with zootechnical and statistical analysis, we aimed to distinguish the microbial taxa related to high mortality rates at a given larval stage.

Results

We highlight that the active microbiota of the rearing water is highly dynamic whatever the larval survival rate. A clear distinction of the microbial composition is shown between the water harboring heathy larvae reared with antibiotics versus the unhealthy larvae reared without antibiotics. However, it is hard to untangle the effects of the antibiotic addition and of the larval death on the active microbiota of the rearing water. Various active taxa of the rearing water are specific to a given larval stage and survival rate except for the zoea with a good survival rate. Comparing these communities to those of the lagoon, it appears that many taxa were originally detected in the natural seawater. This highlights the great importance of the microbial composition of the lagoon on the rearing water microbiota. Considering the larval stage and larval survival we highlight that several genera: Nautella, Leisingera, Ruegerira, Alconivorax, Marinobacter and Tenacibaculum, could be beneficial for the larval survival and may, in the rearing water, overcome the r-strategist microorganisms and/or putative pathogens. Members of these genera might also act as probiotics for the larvae. Marivita, Aestuariicocccus, HIMB11 and Nioella, appeared to be unfavorable for the larval survival and could be associated with upcoming and occurring larval mortalities. All these specific biomarkers of healthy or unhealthy larvae, could be used as early routine detection proxies in the natural seawater and then during the first days of larval rearing, and might help to manage the rearing water microbiota and to select beneficial microorganisms for the larvae.

Microbiota and Cyanotoxin Content of Retail Spirulina Supplements and Spirulina Supplemented Foods

Cyanobacterial biomass such as spirulina (Arthrospira spp.) is widely available as a food supplement and can also be added to foods as a nutritionally beneficial ingredient. Spirulina is often produced in open ponds, which are vulnerable to contamination by various microorganisms, including some toxin-producing cyanobacteria. This study examined the microbial population of commercially available spirulina products including for the presence of cyanobacterial toxins. Five products (two supplements, three foods) were examined. The microbial populations were determined by culture methods, followed by identification of isolates using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF), and by 16S rRNA amplicon sequencing of the products themselves and of the total growth on the enumeration plates. Toxin analysis was carried out by enzyme-linked immunosorbent assay (ELISA). Several potentially pathogenic bacteria were detected in the products, including Bacillus cereus and Klebsiella pneumoniae. Microcystin toxins were detected in all the products at levels that could lead to consumers exceeding their recommended daily limits. Substantial differences were observed in the identifications obtained using amplicon sequencing and MALDI-TOF, particularly between closely related Bacillus spp. The study showed that there are microbiological safety issues associated with commercial spirulina products that should be addressed, and these are most likely associated with the normal means of production in open ponds.

Selecting 16S rRNA Primers for Microbiome Analysis in a Host-Microbe System: The Case of the Jellyfish Rhopilema nomadica

Amplicon sequencing of the 16S rRNA gene is extensively used to characterize bacterial communities, including those living in association with eukaryotic hosts. Deciding which region of the 16S rRNA gene to analyze and selecting the appropriate PCR primers remains a major decision when initiating any new microbiome study. Based on a detailed literature survey of studies focusing on cnidarian microbiomes, we compared three commonly used primers targeting different hypervariable regions of the 16S rRNA gene, V1V2, V3V4, and V4V5, using the jellyfish Rhopilema nomadica as a model. Although all primers exhibit a similar pattern in bacterial community composition, the performance of the V3V4 primer set was superior to V1V2 and V4V5. The V1V2 primers misclassified bacteria from the Bacilli class and exhibited low classification resolution for Rickettsiales, which represent the second most abundant 16S rRNA gene sequence in all the primers. The V4V5 primer set detected almost the same community composition as the V3V4, but the ability of these primers to also amplify the eukaryotic 18S rRNA gene may hinder bacterial community observations. However, after overcoming the challenges possessed by each one of those primers, we found that all three of them show very similar bacterial community dynamics and compositions. Nevertheless, based on our results, we propose that the V3V4 primer set is potentially the most suitable for studying jellyfish-associated bacterial communities. Our results suggest that, at least for jellyfish samples, it may be feasible to directly compare microbial community estimates from different studies, each using different primers but otherwise similar experimental protocols. More generally, we recommend specifically testing different primers for each new organism or system as a prelude to large-scale 16S rRNA gene amplicon analyses, especially of previously unstudied host-microbe associations.

Determining the most accurate 16S rRNA hypervariable region for taxonomic identification from respiratory samples

16S rRNA gene profiling, which contains nine hypervariable regions (V1-V9), is the gold standard for identifying taxonomic units by high-throughput sequencing. Microbiome studies combine two or more region sequences (usually V3-V4) to increase the resolving power for identifying bacterial taxa. We compare the resolving powers of V1-V2, V3-V4, V5-V7, and V7-V9 to improve microbiome analyses in sputum samples from patients with chronic respiratory diseases. DNA were isolated from 33 human sputum samples, and libraries were created using a QIASeq screening panel intended for Illumina platforms (16S/ITS; Qiagen Hilden, Germany). The analysis included a mock community as a microbial standard control (ZymoBIOMICS). We used the Deblur algorithm to identify bacterial amplicon sequence variants (ASVs) at the genus level. Alpha diversity was significantly higher for V1-V2, V3-V4, and V5-V7 compared with V7-V9, and significant compositional dissimilarities in the V1-V2 and V7-V9 analyses versus the V3-V4 and V5-V7 analyses. A cladogram confirmed these compositional differences, with the latter two being very similar in composition. The combined hypervariable regions showed significant differences when discriminating between the relative abundances of bacterial genera. The area under the curve revealed that V1-V2 had the highest resolving power for accurately identifying respiratory bacterial taxa from sputum samples. Our study confirms that 16S rRNA hypervariable regions provide significant differences for taxonomic identification in sputum. Comparing the taxa of microbial community standard control with the taxa samples, V1-V2 combination exhibits the most sensitivity and specificity. Thus, while third generation full-length 16S rRNA sequencing platforms become more available, the V1-V2 hypervariable regions can be used for taxonomic identification in sputum.

Metagenomic data reveals microbiome characteristics of culture-negative brain abscess samples

A brain abscess is a focal collection of pus in the brain parenchyma surrounded by a well-vascularized collagenous capsule in response to an infection. The microbiome of brain abscesses has been shown to be polymicrobial, dominated by uncultivable and anaerobic organisms of odontogenic origin. The data provided in this article includes the sequences of bacterial 16S rRNA gene from three culture-negative brain abscess samples suspected to have poly-microbial aetiology based on Sanger sequencing. DNA was extracted from brain abscess samples, and targeted-metagenomics sequencing was done by amplifying the full-length bacterial 16S rRNA followed by a nested PCR for V3-V4 regions using universal and specific primers. The barcoded amplicons were sequenced on Illumina MiSeq V2 instrument to generate 0.5M, 250bp paired-end reads/sample. The total sequencing reads were 455966, 345746, and 438658 for samples P32, P49, and P8, respectively. Bioinformatics tools such as FLASH, VSEARCH, and QIIME1 were used to process the reads generated for Operational Taxonomic Unit analysis (OTU). Bacterial species belonging to phyla Firmicutes, Bacteroidetes, and Fusobacteria were abundant in samples P49 and P8, which are mainly anaerobic and microaerophilic bacteria. These are typical of the human oral/gut microbiota and are implicated in brain abscess formation. Sample P32 showed the abundance of bacterial species belonging to phyla Proteobacteria and Actinobacteria, which are commonly found in the environment. Raw data files are available at the Sequence Read Archive (SRA), National Center for Biotechnology Information (NCBI), and data information can be found at the BioProject, PRJNA785100 under the accession numbers SRX13271109, SRX13271110, SRX13295897. The data shows the microbiome constitution, including several anaerobic and unculturable bacterial species from culture-negative brain abscess samples. This dataset will be useful for future research on comparative genomics and management of patients with culture-negative brain abscesses.

Characterization of the Gut Microbiota in Urban Thai Individuals Reveals Enterotype-Specific Signature

Gut microbiota play vital roles in human health, utilizing indigestible nutrients, producing essential substances, regulating the immune system, and inhibiting pathogen growth. Gut microbial profiles are dependent on populations, geographical locations, and long-term dietary patterns resulting in individual uniqueness. Gut microbiota can be classified into enterotypes based on their patterns. Understanding gut enterotype enables us to interpret the capability in macronutrient digestion, essential substance production, and microbial co-occurrence. However, there is still no detailed characterization of gut microbiota enterotype in urban Thai people. In this study, we characterized the gut microbiota of urban Thai individuals by amplicon sequencing and classified their profiles into enterotypes, including Prevotella (EnP) and Bacteroides (EnB) enterotypes. Enterotypes were associated with lifestyle, dietary habits, bacterial diversity, differential taxa, and microbial pathways. Microbe-microbe interactions have been studied via co-occurrence networks. EnP had lower α-diversities than those in EnB. A correlation analysis revealed that the Prevotella genus, the predominant taxa of EnP, has a negative correlation with α-diversities. Microbial function enrichment analysis revealed that the biosynthesis pathways of B vitamins and fatty acids were significantly enriched in EnP and EnB, respectively. Interestingly, Ruminococcaceae, resistant starch degraders, were the hubs of both enterotypes, and strongly correlated with microbial diversity, suggesting that traditional Thai food, consisting of rice and vegetables, might be the important drivers contributing to the gut microbiota uniqueness in urban Thai individuals. Overall findings revealed the biological uniqueness of gut enterotype in urban Thai people, which will be advantageous for developing gut microbiome-based diagnostic tools.

Geography, taxonomy, and ecological guild: Factors impacting freshwater macroinvertebrate gut microbiomes

Despite their diversity, global distribution, and apparent effects on host biology, the rules of life that govern variation in microbiomes among host species remain unclear, particularly in freshwater organisms. In this study, we sought to assess whether geographic location, taxonomy (order, family, and genus), or functional feeding group (FFG) designations would best explain differences in the gut microbiome composition among macroinvertebrates sampled across 10 National Ecological Observatory Network's (NEON) freshwater stream sites in the United States. Subsequently, we compared the beta diversity of microbiomes among locations, taxonomy (order, family, and genus), and FFGs in a single statistical model to account for variation within the source microbial community and the types of macroinvertebrates sampled across locations. We determined significant differences in community composition among macroinvertebrate orders, families, genera, and FFGs. Differences in microbiome compositions were underscored by different bacterial ASVs that were differentially abundant among variables (four bacterial ASVs across the 10 NEON sites, 43 ASVs among the macroinvertebrate orders, and 18 bacterial ASVs differing among the five FFGs). Analyses of variations in microbiome composition using the Bray-Curtis distance matric revealed FFGs as the dominant source of variation (mean standard deviation of 0.8), followed by stream site (mean standard deviation of 0.5), and finally family and genus (mean standard deviation of 0.3 each). Our findings revealed a principal role for FFG classification in insect gut microbiome beta diversity with additional roles for geographic distribution and taxonomy.

Differential gut microbiota and intestinal permeability between frail and healthy older adults: A systematic review

This systematic review appraised previous findings on differential gut microbiota composition and intestinal permeability markers between frail and healthy older adults. A literature search was performed using PubMed, Scopus, ScienceDirect and the Cochrane Library. Relevant studies were shortlisted based on inclusion and exclusion criteria as well as assessed for risk of bias. The primary outcome was the differential composition of gut microbiota and/ or intestinal permeability markers between frail and healthy older adults. A total of 10 case-control studies and one cohort study were shortlisted. Based on consistent findings reported by more than one shortlisted study, the microbiota of frail older adults was characterised by decreased phylum Firmicutes, with Dialister, Lactobacillus and Ruminococcus being the prominent genera. Healthy controls, on the other hand, exhibited higher Eubacterium at the genera level. In terms of intestinal permeability, frail older adults were presented with increased serum zonulin, pro-inflammatory cytokines (TNF-α, HMGB-1, IL-6, IL1-ra, MIP-1β) and amino acids (aspartic acid and phosphoethanolamine) when compared to healthy controls. Altogether, frail elderlies had lower gut microbiota diversity and lower abundance of SCFA producers, which may have led to leaky guts, upregulated pro-inflammatory cytokines, frailty and sarcopenia.

Fermented Soybean Meal (FSBM) in African Catfish (Clarias gariepinus) Diets: Effects on Growth Performance, Fish Gut Microbiota Analysis, Blood Haematology, and Liver Morphology

The study revealed the potential of fermented soybean meal (FSBM) as a fish meal (FM) replacement in African catfish (Clarias gariepinus) feed formulation. Five isonitrogenous diets (32% crude protein) were prepared with five different levels of FSBM as FM replacement, namely 0% FSBM (T1), 40% FSBM (T2), 50% FSBM (T3), 60% FSBM (T4), and 70% (T5). The experimental fish was given the formulated diet for eight consecutive weeks. At the end of the feeding trial, the fish were subjected to growth performance, blood parameters, blood chemical, liver histology, and gut microbiota assessment. The study findings demonstrated that the experimental fish that received the T2 diet exhibited significantly higher (p < 0.05) growth performance. Experimental fish that received diet T2 had significantly higher (p < 0.05) white blood cell (WBC) and significantly lower (p < 0.05) in terms of cholesterol (CHOL), albumin (ALB), globulin (GLOB), and total protein (TP). The replacement of FSBM to FM significantly affected liver morphology on the sinusoid, vacuole, nucleus, and erythrocytes. Gut microbiota composition analysis showed a significantly high abundance (p < 0.05) of Akkermansia muciniphila in the experimental fish that received the T2 diet. The gut microbiota indicates that the experimental fish is in a healthy condition. In conclusion, replacing 40% FSBM with FM in aquafeed could enhance C. gariepinus growth performance and health conditions.

Enhancing biohydrogen gas production in anaerobic system via comparative chemical pre-treatment on palm oil mill effluent (POME)

Biological hydrogen production using palm oil mill effluent (POME) as a carbon source through dark fermentation process has been suggested to be a promising bioenergy potential and enacts as alternative renewable energy source. Results have indicated that among various 1.5% (w/v) chemical pre-treatments (sodium hydroxide, NaOH; hydrochloric acid, HCl; sulphuric acid, H₂SO₄; phosphoric acid, H₃PO₄ and nitric acid, HNO₃) on POME, using H₃PO₄ would generate maximum biohydrogen production of 0.193 mmol/L/h, which corresponded to a yield of 1.51 mol H₂/mol TC_consumed with an initial total soluble carbohydrate concentration of 23.52 g/L. Among H₃PO₄ concentrations (1%-10%), the soluble carbohydrate content and the biohydrogen produced was highest and increased by 1.70-fold and 2.35-fold respectively at 2.5% (w/v), as compared to untreated POME. The batch fermentation maximum hydrogen production rate and yield of 0.208 mmol/L/h and 1.69 mol H₂/mol TC_consumed were achieved at optimum pre-treatment conditions of pH 5.5 and thermophilic temperature (60 °C). This study suggests that chemical pre-treatment approaches manage to produce and improve the carbohydrate utilisation process further. Continuous fermentation in CSTR at the optimum conditions produce heightened 1.5-fold biohydrogen yield for 2.5% H₃PO₄ at 6 h HRT as compared to batch scale. Bacterial community via next-generation sequencing analysis at optimum HRT (6 h) revealed that Thermoanaerobacterium thermosaccharolyticum registered the highest relative frequency of 20.24%. At the class level, Clostridia, Bacilli, Bacteroidia, Thermoanaerobacteria, and Gammaproteobacteria were identified as the biohydrogen-producing bacteria in the continuous system. Insightful findings from this study suggest the substantial practical utility of dilute chemical pre-treatment in improving biohydrogen production.

Impact of microcin J25 on the porcine microbiome in a continuous culture model

The increased prevalence of Salmonella spp. resistance in swine spurs the search for alternatives to antibiotics. Microcin J25 (MccJ25), a bacteriocin produced by Escherichia coli, is a potent inhibitor of several pathogenic bacteria including Salmonella enterica. In this study, we aimed to evaluate in vitro the impact of MccJ25 on the composition and the metabolic activity of the swine colonic microbiota. The PolyFermS in vitro continuous fermentation model was used here with modified Macfarlane medium to simulate the porcine proximal colon. During 35 days of fermentation, a first-stage reactor containing immobilized swine fecal microbiota fed two second-stage control and test reactors operated in parallel and used to test the effects of MccJ25 on the composition and the metabolic activity of the microbiota. Reuterin, a broad-spectrum antimicrobial compound produced by Limosilactobacillus reuteri, a lactic acid bacterium naturally present in the gastro-intestinal tract of human and animals, and the antibiotic rifampicin were tested for comparison. Sequencing of 16S rRNA was performed using the Illumina MiSeq technology to evaluate microbial diversity, and liquid chromatography coupled to mass spectrometry (LC-MS) followed by multivariate analysis was used to assess the bacteriocin/antibiotic degradation products and to monitor changes in the swine colonic microbiota metabolome. The results show that MccJ25 or reuterin treatments only induce subtle changes of both the microbial diversity and the metabolome of the swine colon microbiota, while rifampicin induces significant modification in amino acid levels. Although these findings need being validated in vivo, this study affords a first proof of concept for considering MccJ25 as a possible alternative to antibiotics for veterinary and farming applications, taking into account its pathogen-selective and potent inhibitory activity.

Nanopore-based metagenomic analysis of the impact of nanoparticles on soil microbial communities

The current trend of using nanotechnology products in all spheres of human life, including for crop improvement may have a possible impact on soil microorganisms which influence soil and plant health. Nanopore-based metagenomic study reported here used full-length 16S rRNA gene sequences to assess shifts in community composition of soil microorganisms when treated with silver, titanium dioxide and zinc oxide nanoparticles (S-NP, T-NP, Z-NP, respectively). Firmicutes and Proteobacteria were the two dominant phyla in this soil, and there were no significant differences (p < 0.05) observed in these phyla across treatments. However, in the phylum Firmicutes, the abundance of the order Clostridiales showed a significant decrease (p < 0.05) in the presence of S-NP. Similarly, in the phylum Proteobacteria, a significant decrease in the presence of S-NP was seen for two orders, Vibrionales (p < 0.05) and Rhodobacterales (p < 0.01). Analysis at a further depth revealed that abundance of the genus Clostridium (order Clostridiales) decreased in the presence of both S-NP (p < 0.01) and T-NP (p < 0.05). The abundance of the genus Vibrio (order Vibrionales) was likewise impacted in the presence of all the three NPs — S-NP (p < 0.01), T-NP (p < 0.05) and Z-NP (p < 0.05). Analyses at high taxon ranks such as phyla may not give a good representation of the nature of microbial community shifts, and at times may paint an erroneous picture. The use of full-length 16S rRNA gene sequences here yielded a greater taxonomic depth, and some shifts at the lower ranks were discernible.

Agavin induces beneficial microbes in the shrimp microbiota under farming conditions

Prebiotics and probiotics have shown a number of beneficial impacts preventing diseases in cultured shrimps. Complex soluble carbohydrates are considered ideal for fostering microbiota biodiversity by fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPS). Here we evaluated the growth performance and microbiota composition of the white shrimp Litopenaeus vannamei after dietary intervention using agavin as a FODMAP prebiotic under farming conditions. Adult L. vannamei were raised at a shrimp farm and the effect of agavin supplemented at 2% (AG2) or 10% (AG10) levels were compared to an agavin-free basal diet (BD). After 28 days-trial, the feed conversion ratio, total feed ingested, and protein efficiency ratio was significantly improved on animals fed with AG2. At the same time, no effect on growth performance was observed in AG10. Surprisingly, after sequencing the V3-V4 regions of the 16S rRNA gene a higher microbial richness and diversity in the hepatopancreas and intestine was found only in those animals receiving the AG10 diet, while those receiving the AG2 diet had a decreased richness and diversity, both diets compared to the BD. The beta diversity analysis showed a clear significant microbiota clustering by agavin diets only in the hepatopancreas, suggesting that agavin supplementation had a more substantial deterministic effect on the microbiota of hepatopancreas than on the intestine. We analyzed the literature to search beneficial microbes for shrimp's health and found sequences for 42 species in our 16S data, being significantly increased Lactobacillus pentosus, Pseudomonas putida and Pseudomonas synxantha in the hepatopancreas of the AG10 and Rodopseudomonas palustris and Streptococcus thermophiles th1435 in the hepatopancreas of the AG2, both compared to BD. Interestingly, when we analyzed the abundance of 42 beneficial microbes as a single microbial community "meta-community," found an increase in their abundance as agavin concentration increases in the hepatopancreas. In addition, we also sequenced the DNA of agavin and found 9 of the 42 beneficial microbes. From those, Lactobacillus lactis and Lactobacillus delbrueckii were found in shrimps fed with agavin (both AG2 and AG10), and Lysinibacillus fusiformis in AG10 and they were absent the BD diet, suggesting these three species could be introduced with the agavin to the diet. Our work provides evidence that agavin supplementation is associated with an increase of beneficial microbes for the shrimp microbiota at farming conditions. Our study provides the first evidence that a shrimp prebiotic may selectively modify the microbiota in an organ-dependent effect.

Effect of red osier dogwood extract on growth performance, blood biochemical parameters, and gut functionality of broiler chickens challenged or unchallenged intraperitoneally with Salmonella Enteritidis lipopolysaccharide

As we advance in the search for antibiotic-alternatives, harnessing plant materials with high total polyphenol concentration (TPC) would be quintessential. Given the high TPC in red osier dogwood (ROD) extract, the current study aimed to determine its efficacy on the growth performance, intestinal health, blood biochemistry, and antioxidant capacity of broiler chickens. A 21-day 4x2 factorial feeding trial was conducted based on two main factors namely, dietary treatments and Salmonella Enteritidis Lipopolysaccharides SE-LPS) challenge. A total of 384 one-day-old mixed-sex Cobb-500 broiler chicks were randomly allotted to four dietary treatments - Negative control (NC), NC + 0.05% bacitracin methylene disalicylate (BMD), NC + 0.3%ROD, and NC+0.5% ROD. Each treatment was assigned to eight replicates with six birds/replicate. On d 13 and 20, half of the birds were intraperitoneally injected with 1mL phosphate-buffered-saline /kg BW of birds (Unchallenged-group) and the remaining half with 1mg SE-LPS /kg BW of birds (Challenged-group). Average weight gain (AWG), average feed intake (AFI), feed conversion ratio (FCR), and mortality were determined weekly. On d 21, ten chickens/treatment were euthanized for measuring blood biochemical parameters, immune organ weights, caecal SCFA, and caeca microbiota. The SE-LPS decreased (P < 0.05) AWG and FCR on d 14 and 21, respectively. On d 14, 21, and overall basis, both ROD extract levels marginally improved (P < 0.05) the AWG of unchallenged birds compared to other treatments in the unchallenged-group. Challenged and unchallenged birds fed ROD extract had deeper (P < 0.05) crypt depth (CD) and higher villus height:CD, respectively, in the ileum. Globulin (GLB) and albumin:GLB were increased and reduced (P < 0.05), respectively, among birds fed 0.3%ROD compared to other treatments. There was no treatment effect on caeca SCFA, relative weight of immune organs, and serum antioxidants. Birds fed ROD extract had a higher (P < 0.05) relative abundance of caecal Lactobacillus and Streptococcus genera compared to the antibiotic treatment. Conclusively, incorporating 0.3% and 0.5%ROD extract into broiler chickens' nutrition improved growth performance and ileal morphology, and modified caecal microbiota of broiler chickens, regardless of the intraperitoneal SE-LPS challenge.

Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome

Host genetics has recently been shown to be a driver of plant microbiome composition. However, identifying the underlying genetic loci controlling microbial selection remains challenging. Genome-wide association studies (GWAS) represent a potentially powerful, unbiased method to identify microbes sensitive to the host genotype and to connect them with the genetic loci that influence their colonization. Here, we conducted a population-level microbiome analysis of the rhizospheres of 200 sorghum genotypes. Using 16S rRNA amplicon sequencing, we identify rhizosphere-associated bacteria exhibiting heritable associations with plant genotype, and identify significant overlap between these lineages and heritable taxa recently identified in maize. Furthermore, we demonstrate that GWAS can identify host loci that correlate with the abundance of specific subsets of the rhizosphere microbiome. Finally, we demonstrate that these results can be used to predict rhizosphere microbiome structure for an independent panel of sorghum genotypes based solely on knowledge of host genotypic information.

Colorectal Cancer Stage-Specific Fecal Bacterial Community Fingerprinting of the Taiwanese Population and Underpinning of Potential Taxonomic Biomarkers

Despite advances in the characterization of colorectal cancer (CRC), it still faces a poor prognosis. There is growing evidence that gut microbiota and their metabolites potentially contribute to the development of CRC. Thus, microbial dysbiosis and their metabolites associated with CRC, based on stool samples, may be used to advantage to provide an excellent opportunity to find possible biomarkers for the screening, early detection, prevention, and treatment of CRC. Using 16S rRNA amplicon sequencing coupled with statistical analysis, this study analyzed the cause–effect shift of the microbial taxa and their metabolites that was associated with the fecal gut microbiota of 17 healthy controls, 21 polyps patients, and 21 cancer patients. The microbial taxonomic shift analysis revealed striking differences among the healthy control, polyps and cancer groups. At the phylum level, Synergistetes was reduced significantly in the polyps group compared to the healthy control and cancer group. Additionally, at the genus level and in association with the cancer group, a total of 12 genera were highly enriched in abundance. In contrast, only Oscillosprira was significantly higher in abundance in the healthy control group. Comparisons of the polyps and cancer groups showed a total of 18 significantly enriched genera. Among them, 78% of the genera associated with the cancer group were in higher abundance, whereas the remaining genera showed a higher abundance in the polyps group. Additionally, the comparison of healthy control and polyp groups showed six significantly abundant genera. More than 66% of these genera showed a reduced abundance in the polyps group than in healthy controls, whereas the remaining genera were highly abundant in the polyps group. Based on tumor presence and absence, the abundance of Olsenella and Lactobacillus at the genus level was significantly reduced in the patient group compared to healthy controls. The significant microbial function prediction revealed an increase in the abundance of metabolites in the polyps and cancer groups compared to healthy controls. A correlation analysis revealed a higher contribution of Dorea in the predicted functions. This study showed dysbiosis of gut microbiota at the taxonomic level and their metabolic functions among healthy subjects and in two stages of colorectal cancer, including adenoma and adenocarcinoma, which might serve as potential biomarkers for the early diagnosis and treatment of CRC.

Microbiomes of clownfish and their symbiotic host anemone converge before their first physical contact

BACKGROUND

One of the most charismatic, and yet not completely resolved example of mutualistic interaction is the partnership of clownfish and its symbiotic sea anemone. The mechanism explaining this tolerance currently relies on the molecular mimicry of clownfish epithelial mucus, which could serve as camouflage, preventing the anemone's nematocysts' discharge. Resident bacteria are known as key drivers of epithelial mucus chemical signature in vertebrates. A recent study has proposed a restructuration of the skin microbiota in a generalist clown fish when first contacting its symbiotic anemone. We explored a novel hypothesis by testing the effect of remote interaction on epithelial microbiota restructuration in both partners.

METHODS

With metataxonomics, we investigated the epithelial microbiota dynamic of 18 pairs of percula clownfish (Amphiprion percula) and their symbiotic anemone Heteractis magnifica in remote interaction, physical interaction and control groups for both partners during a 4-week trial.

RESULTS

The Physical and Remote Interaction groups' results evidence gradual epithelial microbiota convergence between both partners when fish and anemone were placed in the same water system. This convergence occurred preceding any physical contact between partners, and was maintained during the 2-week interaction period in both contact groups. After the interaction period, community structure of both fish and anemone's epthelial community structures maintained the interaction signature 2 weeks after fish-anemone pairs' separation. Furthermore, the interaction signature persistence was observed both in the Physical and Remote Interaction groups, thus suggesting that water-mediated chemical communication between symbiotic partners was strong enough to shift the skin microbiota durably, even after the separation of fish-anemone pairs. Finally, our results suggest that fish-anemone convergent microbiota restructuration was increasingly associated with the parallel recruitment of three Flavobacteriaceae strains closely related to a tyrosinase-producing Cellulophaga tyrosinoxydans.

CONCLUSIONS

Our study shows that bacterial community restructuration, in the acclimation process, does not only rely on direct physical contact. Furthermore, our results challenge, for the first time, the traditional unidirectional chemical camouflage hypothesis, as we argue that convergence of the epithelial microbiota of both partners may play essential roles in establishing mutual acceptance. Video abstract Fish-anemone symbiotic relationship.

OTUs and ASVs Produce Comparable Taxonomic and Diversity from Shrimp Microbiota 16S Profiles Using Tailored Abundance Filters

The interplay between shrimp immune system, its environment, and microbiota contributes to the organism’s homeostasis and optimal production. The metagenomic composition is typically studied using 16S rDNA profiling by clustering amplicon sequences into operational taxonomic units (OTUs) and, more recently, amplicon sequence variants (ASVs). Establish the compatibility of the taxonomy, α, and β diversity described by both methods is necessary to compare past and future shrimp microbiota studies. Here, we used identical sequences to survey the V3 16S hypervariable-region using 97% and 99% OTUs and ASVs to assess the hepatopancreas and intestine microbiota of L. vannamei from two ponds under standardized rearing conditions. We found that applying filters to retain clusters >0.1% of the total abundance per sample enabled a consistent taxonomy comparison while preserving >94% of the total reads. The three sets turned comparable at the family level, whereas the 97% identity OTU set produced divergent genus and species profiles. Interestingly, the detection of organ and pond variations was robust to the clustering method’s choice, producing comparable α and β-diversity profiles. For comparisons on shrimp microbiota between past and future studies, we strongly recommend that ASVs be compared at the family level to 97% identity OTUs or use 99% identity OTUs, both using tailored frequency filters.

Biodegradation of diisononyl phthalate by a consortium of saline soil bacteria: optimisation and kinetic characterisation

Diisononyl phthalate (DINP) is one of plasticisers most employed in the production of plastic materials and belongs to the most important environmental contaminants. In this work, a consortium of saline soil bacterial (SSB) capable of degrading DINP is presented. The genera of SSB-consortium were Serratia sp., Methylobacillus sp., Achromobacter sp., Pseudomonas sp., Stenotrophomonas sp., Methyloversatilis sp., Delftia sp. and Brevundimonas sp. Response surface methodology (RSM) study was employed to optimise and evaluate the culture conditions to improve the biodegradation of DINP. The optimal conditions were a pH 7.0, 31 °C and an initial DINP concentration of 500 mg L^-1, resulting in almost complete biodegradation (99%) in 168 h. DINP degradation followed a first-order kinetic model, and the half-life was 12.76 h. During the biodegradation of DINP, 4-derived compounds were identified: monoisononyl phthalate, methyl nonyl phthalate, iso-nonanol and dimethyl phthalate. The metabolite profiling indicated that DINP was degraded through simultaneous pathways of de-esterification and β-oxidation. Results suggest that the SSB-consortium could be useful for efficient biodegradation of the DINP-contaminated environments. KEY POINTS: • DINP degradation is mediated by de-esterification and β-oxidation processes. • Temperature and the concentration of the substrate are key factors for DINP biodegradation • The SSB-consortium has the ability to biodegrade 99% of DINP (500 mg L^-1).

Bacillus subtilis delivery route: effect on growth performance, intestinal morphology, cecal short-chain fatty acid concentration, and cecal microbiota in broiler chickens

As the poultry industry recedes from the use of antibiotic growth promoters, the need to evaluate the efficacy of possible alternatives and the delivery method that maximizes their effectiveness arises. This study aimed at expounding knowledge on the effect of the delivery method of a probiotic product (Bacillus subtilis fermentation extract) on performance and gut parameters in broiler chickens. A total of 450 fertile eggs sourced from Cobb 500 broiler breeders were randomly allotted to 3 groups: in ovo probiotic (n = 66), in ovo saline (n = 66), and noninjection (n = 200) and incubated for 21 d. On day 18.5 of incubation, 200 μL of either probiotic (10 × 10⁶ cfu) or saline was injected into the amnion. At hatch, chicks were reallotted to 6 new treatment groups: in ovo probiotic, in ovo saline, in-feed antibiotics, in-water probiotic, in-feed probiotics, and control (corn-wheat-soybean diet) in 6 replicate cages and raised for 28 d. Of all hatch parameters evaluated, only percentage pipped eggs was found significant (P < 0.05) with the noninjection group having higher percentage pipped eggs than the other groups. Treatments did not affect the incidence of necrotic enteritis on day 28 (P > 0.05). Irrespective of the delivery method, the probiotic treatments had no significant effect on growth performance. The ileum villus width of the in ovo probiotic treatment was 18% higher than the in ovo saline group (P = 0.05) but not statistically higher than other groups. The jejunum villus height was 23% higher (P = 0.000) in the in ovo probiotic group than in the control group. There was no effect of treatment on total cecal short-chain fatty acid concentration and cecal gut microbiota composition and diversity (P > 0.05), although few unique bacteria differential abundance were recorded per treatment. Conclusively, although probiotic treatments (irrespective of the delivery route) did not affect growth performance, in ovo delivery of the probiotic product enhanced intestinal morphology, without compromising hatch performance and gut homeostasis.

Understanding the role of the shrimp gut microbiome in health and disease

With rapid increases in the global shrimp aquaculture sector, a focus on animal health during production becomes ever more important. Animal productivity is intimately linked to health, and the gut microbiome is becoming increasingly recognised as an important driver of cultivation success. The microbes that colonise the gut, commonly referred to as the gut microbiota or the gut microbiome, interact with their host and contribute to a number of key host processes, including digestion and immunity. Gut microbiome manipulation therefore represents an attractive proposition for aquaculture and has been suggested as a possible alternative to the use of broad-spectrum antibiotics in the management of disease, which is a major limitation of growth in this sector. Microbiota supplementation has also demonstrated positive effects on growth and survival of several different commercial species, including shrimp. Development of appropriate gut supplements, however, requires prior knowledge of the host microbiome. Little is known about the gut microbiota of the aquatic invertebrates, but penaeid shrimp are perhaps more studied than most. Here, we review current knowledge of information reported on the shrimp gut microbiota, highlighting the most frequently observed taxa and emphasizing the dominance of Proteobacteria within this community. We discuss involvement of the microbiome in the regulation of shrimp health and disease and describe how the gut microbiota changes with the introduction of several economically important shrimp pathogens. Finally, we explore evidence of microbiome supplementation and consider its role in the future of penaeid shrimp production.