Host–bacterial communities (microbiomes) are influenced by a wide range of factors including host genotype and parasite exposure. However, few studies disentangle temporal and host-genotype-specific variation in microbiome response to infection across several host tissues. We experimentally exposed the freshwater crustacean Daphnia magna to its fungal parasite Metschnikowia bicuspidata and characterized changes in host–bacterial communities associated with the parasite's development within the host. We used 16S rRNA gene sequencing to assess bacterial communities of the host (a) 24 h (‘initial parasite exposure’) and (b) 10 days (‘successful infection’) after exposure to a standard dose of M. bicuspidata spores, in host guts, body tissue (excluding guts) and whole individuals. We also investigated whether bacterial community responses to parasite exposure varied by host genotype.

Parasite exposure did not immediately alter host gut bacterial communities, but drove host-genotype-specific changes in the bacterial community composition of whole individuals. We validated that these changes were not driven by shifts in bacterial communities of the culturing medium, due to the addition of the parasite spore solution. Successful infection (i.e. the proliferation of M. bicuspidata spores in the host body) reduced alpha diversity and shifted abundance of dominant bacterial orders in the gut. Moreover, it induced a host-genotype-specific changes in body bacterial community composition. Overall, bacterial community responses to parasite exposure and subsequent infection are complex: they occur in a host-genotype-dependent manner, differentially at distinct timepoints after parasite exposure, and in specific host tissue.

The diversity and health of insects that feed on plants are closely related to their mutualistic symbionts and host plants. These symbiotic partners significantly influence various metabolic activities in these insects. However, the symbiotic bacterial community of toxic plant feeders still needs further characterisation. This study aims to unravel bacterial communities associated with the different species of insect representing three insect orders: Thysanoptera, Hemiptera, and Lepidoptera, along with their predicted functional role, which exclusively feeds on latex-rich plant species Ficus microcarpa. By using 16S rRNA gene high-throughput sequencing, the analysis was able to define the major alignment of the bacterial population, primarily comprising Proteobacteria, Firmicutes, Bacteroidota, Actinobacteriota, and Acidobacteriota. Significant differences in symbiotic organisms between three insect groups were discovered by the study: hemipterans had Burkholderia and Buchnera, and lepidopterans had Acinetobacter. At the same time, Pseudomonas was detected in high abundance in both lepidopteran and thysanopteran insects. Furthermore, these symbionts exhibit consistent core functions, potentially explaining how different insects can consume the same host plant. The identified core functions of symbionts open avenues for innovative approaches in utilising these relationships to develop environment-friendly solutions for pest control, with broader implications for agriculture and environmental conservation.

Egg masses from an unknown mollusc have been found in South-West Iceland since 2020, but it was not until September 2023 that the adult organism was collected. Morphological analysis of both adults and egg masses pointed towards the identification of the species as Melanochlamys diomedea. This was further confirmed through DNA analyses using COI, H3, and 16S rRNA markers, which established the presence of a new non-indigenous species in the North Atlantic. Members of the genus Melanochlamys have predominantly been found in the Indo-Pacific basin and the Pacific Ocean, with only one species known to exist across the Madeira Islands, Canary Islands, and Cape Verde in the Atlantic. The known distribution range of M. diomedea extends from Alaska to California on the Pacific side of North America, where it typically inhabits sandy-muddy areas of the littoral in the tidal zone and below. It is not known how the species arrived in Iceland. However, maritime transport through either ballast water or biofouling is being considered as the most likely mode of dispersal.

Mantis shrimps are commercially important crustaceans in many areas of the world. In contrast to the relatively common studies of adults, limited studies have been attempted of larvae because of a lack of identification keys. The objectives of this study were two-fold: (1) to link wild-caught larval specimens from the Seto Inland Sea to a certain species and (2) to present a detailed morphological description of the last larval stage. The resulting molecular phylogenetic tree based on 16S rRNA gene sequences strongly implies that our larval specimens were linked to Levisquilla inermis, which was barcoded from a newly collected adult specimen with a morphological identification. K2P genetic divergence was found to be 0% among the larval and adult specimens. The congeneric species L. jurichi was the sister group of the L. inermis cluster, but the K2P distance between them was 3.4%, and it was considered a distinct species. Morphological observations provided five major distinguishing characteristics of the last-stage larva of L. inermis: (1) propodus of second maxilliped with three basal spines, (2) all five pleopods possessing an appendix interna with cincinnuli, (3) exopod of uropod longer than the endopod, (4) distal margin of the exopod of the uropod reaching the lateral tooth of telson, and (5) telson with nine intermediate denticles. Overall, our results reveal the importance of combining molecular and morphological analyses for solving stomatopod larval identification. This finding can be used to support and facilitate future research on the taxonomy and biodiversity of stomatopod larvae.

A new fast-growing mycobacterium, designated strain QGD101T, was isolated from the sputum of an 84-year-old man suspected of tuberculosis in Wuhan Medical Treatment Center, Hubei, China. This strain was a gram-staining-negative, aerobic, non-spore-forming and catalase-positive bacterium, which was further identified as the NTM by PNB and TCH tests. The moxifloxacin and levofloxacin exhibited strong suppressing function against QGD101T with MIC values of 0.06 and 0.125 µg/ml after drug susceptibility testing of six main antimicrobial agents on mycobacteria. Based on the sequence analysis of 16S rRNA, rpoB, hsp65 and 16S-23S rRNA internal transcribed spacer, the strain QGD101T could not be identified to a species level. Mycobacterium moriokaense ATCC43059T that shared the highest 16S rRNA gene sequence similarity (98%) with strain QGD101T was actually different in genomes average nucleotide identity (78.74%). In addition, the major cellular fatty acids of QGD101T were determined as C18:1ω9c, C16:0 and C18:2ω6c. The DNA G + C content was 64.9% measured by high performance liquid chromatography. Therefore, the phenotypic and genotypic characterisation of this strain led us to the conclusion that it represents a novel species of mycobacteria, for which the name Mycobacterium hubeiense sp. nov. (type strain QGD101T = CCTCCAA 2017003T = KCTC39927T) was proposed. Thus, the results of this study are very significant for the clinical diagnosis of tuberculosis and future personalised medicine.

Wheat bran (WB) is an important side product of the milling industry and can serve as dietary fiber compound for monogastric animals. The aim of this study was to evaluate the influence of native or fermented WB on the gut physiology and microbiology of laying hens. To accomplish this, 24 laying hens were fed the following diets: conventional diet without WB; 15% native WB in the diet; 15% WB fermented with Pleurotus eryngii; and 15% WB fermented with P. eryngii and a lactic acid bacterial culture. Immediately after slaughtering, digesta samples were taken from the jejunum, ileum and cecum, respectively. Total DNA was extracted and subsequently investigated with 16S DNA amplicon sequencing. Neither native nor fermented WB supplementations negatively affected the feed conversion ratio, laying performance or the relative abundances and alpha-diversity of microbiota in the intestine. Effects of WB-based diets on gut morphology were only recognized in the jejunum (reduced villum height and mucosa thickness). Likewise, WB supplementation decreased the digestibility of DM and starch. Based on these findings, it was demonstrated that different WB variants are applicable without exerting practically negative consequences on performance or on gut microbiota. Fermentation improved the digestibility/retention of dietary fat and phosphorus. However, no further beneficial effects were observed. This study also allowed a more in-depth view on the laying hens’ gut microbiome and its variation within the gut segments.

Exploring the composition and structure of the faecal microbial community improves the understanding of the role of the gut microbiota in the gastrointestinal function and the egg-laying performance of hens. Therefore, detection of hen–microbial interactions can explore a new breeding marker for the selection of egg production due to the important role of the gut microbiome in the host’s metabolism and health. Recently, the gut microbiota has been recognised as a regulator of host performance, which has led to investigations of the productive effects of changes in the faecal microbiome in various animals. In the present study, a metagenomics analysis was applied to characterise the composition and structural diversity of faecal microbial communities under two selections of egg-laying performance, high (H, n = 30) and low (L, n = 30), using 16S rRNA-based metagenomic association analysis. The most abundant bacterial compositions were estimated based on the operational classification units among samples and between the groups from metagenomic data sets. The results indicated that Firmicutes phylum has higher significant (P < 0.01) in the H group than in the L group. In addition, higher relative abundance phyla of Bacteroides and Fusobacteria were estimated in the H group than the L group, contrasting the phyla of Actinobacteria, Cyanobacteria and Proteobacteria were more relative abundance in the L group. The families (Lactobacillus, Bifidobacterium, Acinetobacter, Flavobacteriaceae, Lachnoclostridum and Rhodococcus) were more abundant in the H group based on the comparison between the H and L groups. Meanwhile, three types of phyla (Proteobacteria, Actinobacteria and Cyanobacteria) and six families (Acinetobacter, Avibacterium, Clostridium, Corynebacterium, Helicobacter and Peptoclostridium) were more abundant in the L group (P < 0.01). Overall, the selection of genotypes has enriched a relationship between the gut microbiota and the egg-laying performance. These findings suggest that the faecal microbiomes of chickens with high egg-laying performance have more diverse activities than those of chickens with low egg-laying performance, which may be related to the metabolism and health of the host and egg production variation.

The rapid shift to high-grain (HG) diets in ruminants can affect the function of the rumen epithelium, but the dynamic changes in the composition of the epithelium-associated (epimural) bacterial community in sheep still needs further investigation. Twenty male lambs were randomly allocated to four groups (n = 5). Animals of the first group received hay diet and represented a control group (CON). Simultaneously, animals in the other three groups (HG groups) were rapidly shifted to an HG diet (60% concentrate)which continued for 7 (HG7), 14 (HG14) and 28 (HG28) days, correspondingly. Results showed that ruminal pH dramatically decreased due to the rapid shift to the HG diet (P <0.001), while, the concentrations of butyrate (P <0.001), lactate (P = 0.001), valerate (P = 0.008) and total volatile fatty acids (P = 0.001) increased. Diversity estimators showed a dramatic decrease after the shift without recovering as the HG feeding continued. The principal coordinates analysis showed that CON group clustered separately from all HG groups with the presence of significant difference only between HG7 and HG28 (P = 0.034). The non-parametric multivariate analysis (npmv R-package) deduced that the primary significant differences in phyla and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt)-predicted Kyoto Encyclopedia of Genes and Genomes (KEGGs) was attributed mainly to the diet composition (P <0.001, P = 0.001) compared to its application period (P = 0.140, 0.545) which showed a significant effect only on the genus (P = 0.001) and the operational taxonomic units (OTUs) level (P = 0.011). The Kruskal–Wallis test deduced that six phyla showed a significant effect due to the shift in diet composition. At the genus level, HG feeding altered the abundance of 12 taxa, four of which showed a significant variation due to the duration of the HG diet application. Similarly, we found that 21 OTUs showed significant variations due to the duration of the HG diet application. Furthermore, the genes abundance predicted by PICRUSt revealed that the HG feeding significantly affected seven metabolic pathways identified in the KEGG. Particularly, the abundance of gene families associated with carbohydrates metabolism were significantly higher in HG feeding groups (P = 0.027). Collectively, these results revealed that the rapid transition to an HG diet causes dramatic alterations in ruminal fermentation and the composition and function of ruminal epithelium-associated microbiome in sheep, while, the duration of the HG diet application causes drastic alterations to the abundance of some species.

Population growth, in vitro, of three Paramoeba perurans cultures, one polyclonal (G) and two clonal (B8, CE6, derived from G), previously shown to differ in virulence (B8 > G > CE6), was compared at 10 and 15 °C. B8 showed a significantly higher increase in attached and in suspended amoebae over time at 15 and 10 °C, respectively. CE6 and G also had significantly higher numbers of suspended amoebae at 10 °C compared with 15 °C at experiment termination. However, in contrast to B8, numbers of attached amoebae were significantly higher at 10 °C in CE6 but showed a similar trend in G at the end of the experiment. Numbers of both suspended and attached amoebae were lower in B8 compared with CE6 and G. Significant differences in bacterial community composition and/or relative abundances were found, between cultures, between temperatures and between the same culture with and without amoebae, based on 16S rRNA Illumina MiSeq sequencing. Bacterial diversity was lower in B8 and CE6 compared with G, possibly reflecting selection during clonal isolation. The results indicate that polyclonal P. perurans populations may contain amoebae displaying different growth dynamics. Further studies are required to determine if these differences are linked to differences seen in the bacterial communities.

The heteronemertean species Micrura dellechiajei is thus far only known from its type locality in the Gulf of Naples (Italy) and has not been recorded in 120 years. During two oceanographic surveys conducted in Spanish Mediterranean waters, several nemertean specimens were collected, and thorough morphological examination indicated that some of these pertained to the species M. dellechiajei, suggesting that populations may be more widespread than previously thought. Because of the rarity of this species coupled with the fact that its last morphological narrative was given 120 years ago, we here provide a redescription of the species based on the new specimens, complete with illustrations and new data concerning its morphology, and we also place some of the collected specimens in a molecular phylogenetic framework.

A real-time polymerase chain reaction (PCR) assay was developed for the identification and quantification of two oyster species: Ostrea edulis and Crassostrea gigas. Two sets of primers and TaqMan-MGB probes were designed, based on partial sequences of the 16S rRNA gene. An amplification positive control system was also located in the 18S rRNA gene sequences. Closely related species of oysters and other bivalves, known to co-occur with the target species in European waters, were used to test the assay for cross-reactivity. The assay designed was specific for the target species and no signal or no significant signal was detected for all non-target species tested. The high sensitivity of this method was demonstrated since it is possible to detect just one larva (150–200 μm size) of each species even when it is present with others. Furthermore, this assay provided an acceptable quantification of the number of spiked larvae (1, 10 and 100 larvae) in plankton samples employing a standard curve for larvae.

Host and dietary interactions with the rumen microbiome can affect the efficacy of supplements, and their effect on the composition of the bacterial population is still unknown. A 16S rRNA metagenomic approach and Next-Generation Sequencing (NGS) technology were used to investigate the bacterial microbiome composition in the liquid fraction of the rumen content collected via stomach tubing. To investigate biodiversity, samples were taken from three groups of four lactating dairy cows given a supplement of either 50 g of potato protein (Ctrl group), or 50 g of lyophilized Saccharomyces cerevisiae (LY group) or 50 g of dried S. cerevisiae (DY group) in a potato protein support. Rumen samples were collected after 15 days of dietary treatments and milk production was similar between the three groups. Taxonomic distribution analysis revealed a prevalence of the Firmicutes phylum in all cows (79.76%) and a significantly (P<0.05) higher presence of the genus Bacillus in the DY group. Volatile fatty-acid concentration was not significantly different between groups, possibly because of relatively high inter-animal variability or limited effect of the treatments or both, and the correlation analysis with bacterial taxa showed significant associations, in particular between many Firmicutes genera and butyrate. Limited differences were observed between dietary treatments, but the lack of microbiome data before yeast administration does not allow to draw firm conclusions on the effect of dietary treatments.

Although the beneficial effects of endophytic bacteria on their host are significant, the investigation of the microbial diversity in any Antarctic moss has been neglected. In this study, we investigate the endophytic bacterial diversity of the upper green part and the lower brown part of Sanionia uncinata through 16S rRNA genes using pyrosequencing. Proteobacteria was the most dominant phylum with 65.6%, followed by Bacteroidetes (29.1%) and Actinobacteria (11.7%). The different distribution of Alphaproteobacteria between the upper green (2%) and lower brown (22.2%) parts of the moss was significant. Furthermore, dominant and diverse species were detected and closely related to the environmental sequences. These findings suggest that there are likely to be specific relationships between endophytes and host Antarctic moss species.

The recently inaugurated Belgian Princess Elisabeth Station has been built in the Sør Rondane Mountains (Dronning Maud Land). The construction site is situated close to the Utsteinen Nunatak (71°57′S, 23°20′E), on a granite ridge. Prior to the survey and construction activities, the site had been subject to limited or no direct human impacts. Therefore, a biological inventory has been started for future evaluations of human impacts in the area. This study presents the cyanobacterial diversity of ten samples from the Utsteinen ridge, the Utsteinen Nunatak in the vicinity of the station's site and the more distant Ketelersbreen Dry Valley. All samples were taken before the station was built and were studied by light microscopy and Denaturing Gradient Gel Electrophoresis. Two strains were also isolated. Two different phenol-based extraction methods, with and without detergent-based steps, were tested to improve the quality of molecular detection from these environmental samples. We observed high cyanobacterial diversity (ten morphotypes and 13 operational taxonomic units) in comparison to other Antarctic terrestrial locations and a widespread distribution pattern within the Sør Rondane Mountains area. This might reflect the habitat similarities and/or the easy local dispersal capabilities of microorganisms within the region. The high diversity and proportion of potential endemic (46%) operational taxonomic units, of which 23% were newly described, suggest that this area could have acted as a biological refuge during past glaciations.

The McMurdo Dry Valleys possess a cold and dry climate which favours biomolecular preservation, and present the possibility for preservation of biological materials over long timescales. We examined patterns of bacterial DNA abundance and diversity in algal mats from 8–26 539 years of age. Bacterial DNA abundance was inferred from extractable DNA quantity and quantitative polymerase chain reaction targeting the bacterial 16S rRNA gene. Because damage to bacterial DNA could limit its availability for polymerase chain reaction, the efficacy of DNA repair by a commercially available kit was also examined. Polymerase chain reaction amplicons of the bacterial 16S rRNA gene were obtained from seven of eight samples. Bulk DNA abundance and bacterial 16S rRNA gene copy number of template DNA declined with increasing sample age consistent with expectations of accumulation of DNA damage in ancient materials. Clone libraries revealed age related patterns of abundance for some bacterial phylogenetic groups. For example, Firmicutes and several other lineages were abundant in ancient samples, but Cyanobacteria were absent. This points to a biased persistence of bacterial lineages that change over time since photosynthesis was active.

Archaea, once thought to be only extremophiles, are now known to be abundant in most environments. They can predominate in microbial communities and be significantly involved in many global biogeochemical cycles. However, Archaea have not been reported in Antarctic sea ice. Our understanding of the ecology of Antarctic sea ice prokaryotes is still in its infancy but this information is important if we are to understand their diversity, adaptations and biogeochemical roles in Antarctic systems. We detected Archaea in sea ice at two sampling sites taken from three subsequent years using conserved 16S rRNA gene archaeal primers and PCR. Archaeal abundance was measured using quantitative PCR and community diversity was investigated by sequencing cloned 16S rRNA gene PCR products. Archaea in Antarctic sea ice were found to be in low abundance consisting of ≤ 6.6% of the prokaryotic community. The majority, 90.8% of the sequences, clustered with the recently described phylum Thaumarchaeota, one group closely clustered with the ammonia-oxidizing Candidatus Nitrosopumilus maritimus. The remainder of the clones grouped with the Euryarchaeota.

In French Polynesia, the black-lip pearl oyster Pinctada margaritifera has been farmed to produce pearls since the 1980s, forming the basis of a major industry. The sustainability of this activity relies on spat collection in the lagoons. However, pearl oyster spat can be difficult to identify for the evaluation of stock variations. It is especially hard to distinguish Pinctada spp. larvae at a very early stage of development. In the present study, a whole-mount in situ hybridisation (ISH) technique was developed to allow the discrimination of larvae of closely-related pearl oyster species found in the French Polynesian atolls. Using specific ribosomal 16S-DNA sequence data, we were able to successfully differentiate between Pinctada margaritifera and Pinctada maculata larvae from 5 to 13 days old. This is the first description of a non-destructive method allowing bivalve larvae discrimination between species within this genus. The method allowed us to successfully identify P. margaritifera larvae in natural plankton samples. This result is a key step needed to develop monitoring of P. margaritifera larval distribution in French Polynesian lagoons, a procedure which will increase spat collection efficiency and ensure sustainable development of pearl oyster farming.

Restriction fragment length polymorphism analysis of two segments of mitochondrial DNA (COI and 16S rRNA) was used to examine genetic variation in Sesamia nonagrioides (Lefèbvre) populations from the Mediterranean basin. Four populations were collected from central and southern Greece, and five from northern latitudes: Greece, Italy, France and Spain. No variation was observed in COI, while 16S rRNA segment proved highly polymorphic and 28 different haplotypes were found. Lower intra-population polymorphism was found in the northern populations than in southern ones. Although no significant isolation by distance was found, the UPGMA tree based on Nei's raw number of nucleotide differences separated the populations into two major groups, i.e. one with the northern (40.6°N–43.4°N) and the other with the southern populations (37.3°N–39.2°N). Analysis of molecular variance revealed that most of the variation was between the two major groups (ΦCT=0.559), and all pairwise comparisons between the northern and southern populations resulted in high and significant FST values (overall FST=0.604). The high FST values and the strong spatial genetic structure indicate that long-distance migration may be a rare event. The populations do not seem to have experienced a strong historical bottleneck. The occurrence of a few widespread haplotypes and the genetic similarity of the northern populations could be attributed to a historical expansion of certain haplotypes from the south towards to the northern borders of the species' distribution area.

Bovine mastitis caused by Streptococcus agalactiae is mainly subclinical and therefore can be diagnosed only in the laboratory. A nested polymerase chain reaction (PCR)-based method for specific, sensitive and rapid detection of S. agalactiae in raw milk was developed. The general streptococci primers, which anneal to conserved areas within the 16S rRNA subunit gene, were used as positive controls. The specificity of S. agalactiae primers is based on various areas within conserved areas of the 16S rRNA genes of S. agalactiae. Results have indicated that the method enables the detection of 1 CFU/ml of S. agalactiae in raw milk after enrichment, followed by DNA extraction using a rapid and simple procedure developed for this purpose, and specific PCR reaction. The method developed can be used efficiently in the early infectious status investigation of S. agalactiae in the dairy herd and in prevention and control of S. agalactiae spread in a herd.

In the present study the evolutionary relationships among Cordylusniger–oelofseni–cordylus are investigated using molecular sequence data to: (1) estimate the divergence within this group; (2) date the origin of melanism in the clade and to evaluate possible palaeoecological events responsible for its evolution; (3) examine the systematic relationships among the three isolated populations of C. oelofseni that were previously shown to be polyphyletic using allozyme data. The recovered topology for the combined sequence data (16S and NADH dehydrogenase component 2 (ND2)) among C. niger–oelofseni–cordylus suggests that melanism evolved only once in the clade. The application of a molecular clock to the data demonstrates that melanism evolved during the Miocene epoch, 17–15 million years ago. We believe that the development of a cold-water current and upwelling system along the south-west coast of Africa during this epoch was instrumental in the evolution of melanism in this lizard clade and possibly also in other ectotherm clades with melanistic forms occurring in the area. The results show that C. oelofseni, as presently construed, is composed of three distinct evolutionary lineages, with no shared haplotypes present and marked sequence divergence. Two of the three lineages represent undescribed species. Cordylus cordylus is composed of two distinct clades, a montane clade and a coastal lowland clade. Cladogenic activity in mountain areas of the Western Cape in South Africa has been particularly pronounced and the systematic diversity of many taxa may have been underestimated.