Isolation and characterization of mimosine, 3, 4 DHP and 2, 3 DHP degrading bacteria from a commercial rumen inoculum

Association of maternal genetics with the gut microbiome and eucalypt diet selection in captive koalas

Background

Koalas, an Australian arboreal marsupial, depend on eucalypt tree leaves for their diet. They selectively consume only a few of the hundreds of available eucalypt species. Since the koala gut microbiome is essential for the digestion and detoxification of eucalypts, their individual differences in the gut microbiome may lead to variations in their eucalypt selection and eucalypt metabolic capacity. However, research focusing on the relationship between the gut microbiome and differences in food preferences is very limited. We aimed to determine whether individual and regional differences exist in the gut microbiome of koalas as well as the mechanism by which these differences influence eucalypt selection.

Methods

Foraging data were collected from six koalas and a total of 62 feces were collected from 15 koalas of two zoos in Japan. The mitochondrial phylogenetic analysis was conducted to estimate the mitochondrial maternal origin of each koala. In addition, the 16S-based gut microbiome of 15 koalas was analyzed to determine the composition and diversity of each koala's gut microbiome. We used these data to investigate the relationship among mitochondrial maternal origin, gut microbiome and eucalypt diet selection.

Results and Discussion

This research revealed that diversity and composition of the gut microbiome and that eucalypt diet selection of koalas differs among regions. We also revealed that the gut microbiome alpha diversity was correlated with foraging diversity in koalas. These individual and regional differences would result from vertical (maternal) transmission of the gut microbiome and represent an intraspecific variation in koala foraging strategies. Further, we demonstrated that certain gut bacteria were strongly correlated with both mitochondrial maternal origin and eucalypt foraging patterns. Bacteria found to be associated with mitochondrial maternal origin included bacteria involved in fiber digestion and degradation of secondary metabolites, such as the families Rikenellaceae and Synergistaceae. These bacteria may cause differences in metabolic capacity between individual and regional koalas and influence their eucalypt selection.

Conclusion

We showed that the characteristics (composition and diversity) of the gut microbiome and eucalypt diet selection of koalas differ by individuals and regional origins as we expected. In addition, some gut bacteria that could influence eucalypt foraging of koalas showed the relationships with both mitochondrial maternal origin and eucalypt foraging pattern. These differences in the gut microbiome between regional origins may make a difference in eucalypt selection. Given the importance of the gut microbiome to koalas foraging on eucalypts and their strong symbiotic relationship, future studies should focus on the symbiotic relationship and coevolution between koalas and the gut microbiome to understand individual and regional differences in eucalypt diet selection by koalas.

Causal relationships between gut microbiota and hypothyroidism: a Mendelian randomization study

BACKGROUND

Previous studies have shown that the gut microbiota plays an important role in the maintenance of thyroid homeostasis. We aimed to evaluate the causal relationships between gut microbiota and hypothyroidism.

METHODS

Summary statistics for 211 gut microbiota taxa were obtained from the largest available genome-wide association study (GWAS) meta-analysis conducted by the MiBioGen consortium. Summary statistics for hypothyroidism were obtained from two distinct sources: the FinnGen consortium R9 release data (40,926 cases and 274,069 controls) and the UK Biobank data (22,687 cases and 440,246 controls), respectively. A two-sample Mendelian randomization (MR) design was employed, and thorough sensitivity analyses were carried out to ensure the reliability of the results.

RESULTS

Based on the FinnGen consortium, we found increased levels of Intestinimonas (OR = 1.09; 95%CI = 1.02-1.16; P = 0.01) and Ruminiclostridium5 (OR = 1.11; 95%CI = 1.02-1.22; P = 0.02) may be associated with a higher risk of hypothyroidism, while increased levels of Butyrivibrio (OR = 0.95; 95%CI = 0.92-0.99; P = 0.02), Eggerthella (OR = 0.93; 95%CI = 0.88-0.98; P = 0.01), Lachnospiraceae UCG008 (OR = 0.92; 95%CI = 0.85-0.99; P = 0.02), Ruminococcaceae UCG011 (OR = 0.95; 95%CI = 0.90-0.99; P = 0.02), and Actinobacteria (OR = 0.88; 95%CI = 0.80-0.97; P = 0.01) may be associated with a lower risk. According to the UK Biobank data, Eggerthella and Ruminiclostridium5 remain causally associated with hypothyroidism. The sensitivity analysis demonstrates consistent results without evidence of heterogeneity or pleiotropy.

CONCLUSION

This study highlights the impact of specific gut microbiota on hypothyroidism. Strategies to change composition of gut microbiota may hold promise as potential interventions.

The koala gut microbiome is largely unaffected by host translocation but rather influences host diet

Introduction

Translocation is a valuable and increasingly used strategy for the management of both threatened and overabundant wildlife populations. However, in some instances the translocated animals fail to thrive. Differences in diet between the source and destination areas may contribute to poor translocation outcomes, which could conceivably be exacerbated if the animals' microbiomes are unsuited to the new diet and cannot adapt.

Methods

In this study we tracked how the faecal microbiome of a specialist Eucalyptus folivore, the koala (Phascolarctos cinereus), changed over the course of a year after translocation. We assessed microbiome composition by 16S rRNA amplicon sequencing of faecal pellets.

Results

We found no significant overall changes in the faecal microbiomes of koalas post-translocation (n = 17) in terms of microbial richness, diversity or composition when compared to the faecal microbiomes of koalas from an untranslocated control group (n = 12). This was despite the translocated koalas feeding on a greater variety of Eucalyptus species after translocation. Furthermore, while differences between koalas accounted for half of the microbiome variation, estimated diets at the time of sampling only accounted for 5% of the variation in the koala microbiomes between sampling periods. By contrast, we observed that the composition of koala faecal microbiomes at the time of translocation accounted for 37% of between koala variation in post-translocation diet. We also observed that translocated koalas lost body condition during the first month post-translocation and that the composition of the koalas' initial microbiomes were associated with the magnitude of that change.

Discussion

These findings suggest that the koala gut microbiome was largely unaffected by dietary change and support previous findings suggesting that the koala gut microbiome influences the tree species chosen for feeding. They further indicate that future research is needed to establish whether the koalas' gut microbiomes are directly influencing their health and condition or whether aspects of the koala gut microbiomes are an indicator of underlying physiological differences or pathologies. Our study provides insights into how animal microbiomes may not always be affected by the extreme upheaval of translocation and highlights that responses may be host species-specific. We also provide recommendations to improve the success of koala translocations in the future.

Changes in the bacterial community colonizing extracted and non-extracted tannin-rich plants in the rumen of dromedary camels

Leguminous trees and saltbushes provide potential alternatives to conventional feeds to overcome feed deficiency in arid and semi-arid countries. However, these plants are rich in antinutritional factors that have adverse effects on rumen microbiota and the host- animal. Some rumen microbiota detoxifies plants' secondary metabolites; thus, understanding plant-microbe interaction in the rumen could improve the plants' utilization. This study investigated the bacterial colonization and degradation of non-extracted and extracted tanniniferous plants: Atriplex halimus, Acacia saligna, and Leucaena leucocephala, in the rumen of three fistulated camels at 6 and 12 hours. The results showed that these plants have high nutritional value and tannins contents. The rumen degradation and microbial diversity of plant-attached bacteria varied according to plant type and phenols' extraction. Atriplex and leucaena showed higher microbial diversity at 6 and 12h, respectively. Bacteroidetes and Firmicutes were the main bacterial phyla, and the main genera were Prevotella, RC9_gut_group, Butyrivibrio that overrepresented in non-extracted plants (P<0.05). Fibrobacteres and Anaerovibrio showed sensitivity to plant toxins and Ruminococcus attached to plants with lower tannins. Several bacterial genera in the camel rumen have the potential to resist antinutritional factors in fodder plants, which could be used to improve the performance of grazing animals.

In vitro rumen degradability of tropical legumes and their secondary metabolites depends on inoculum source

In this study, the in vitro apparent rumen degradability of organic matter (ARDOM) and plant secondary metabolites (ARDPSM) of three tropical legumes (Mucuna pruriens, Canavalia ensiformis, and Leucaena leucocephala) were assessed. For this, 3 experiments were set up, i.e., single end-point incubations (24 h) with ruminal inoculum from either Belgian or Cuban sheep, as well as kinetic assessments (0 h, 2 h, 4 h, 6 h, 8 h, 10 h, 12 h, and 24 h) inoculum from Belgian sheep. L-mimosine, L-canavanine, Concanavalin A (Con A), and trypsin inhibitor (TI) were the plant secondary metabolites (PSM) targeted in this study. In all three experiments, both beans, as well as forage/bean meals of M. pruriens and C. ensiformis and their PSM, were extensively degraded during 24 h incubation, irrespective of the inoculum source (0.44 to 0.70 and 0.43 to 0.78 g/g of organic matter (OM) for ARDOM, respectively, and > 0.80 g/g for L-canavanine, > 0.76 TIU/TIU for TI, and > 0.95 g/g for Con A, for both legumes). Forage meal of L. leucocephala was considerably less degraded, with apparent ruminal degradabilities of 0.20 g/g OM and 0.35 g/g OM after 24 h incubation with Belgian or Cuban sheep inoculum, respectively. This could - at least partially - be related to L-mimosine, present in L. leucocephala, which was hardly degraded in the Belgian incubation, while a more extensive ruminal breakdown was observed under the Cuban conditions (0.05 g/g PSM vs. 0.78 g/g PSM, respectively). The negative effect of L-mimosine on OM degradability was supported in an additional in vitro experiment with straw and inoculum from Belgian sheep, as ruminal degradation of straw was 31% lower when pure L-mimosine was supplemented.

Demonstrating the role of symbionts in mediating detoxification in herbivores

Plant toxins constitute an effective defense against herbivorous animals. However, many herbivores have evolved adaptations to cope with dietary toxins through detoxification, excretion, sequestration, target site insensitivity and/or via behavioral avoidance. While these adaptations are often directly encoded in herbivore genomes, evidence is accumulating that microbial symbionts can reduce the dose of plant toxins by metabolizing or sequestering them prior to absorption by the herbivore. Here, we describe a few well-studied examples to assess such symbiont-mediated detoxification and showcase different approaches that have been used for their analyses. These include: (i) a host phenotypic route in which the symbiotic association is manipulated to reveal host fitness costs upon toxin exposure in the presence/absence of detoxifying symbionts, including function restoration after symbiont re-infection, (ii) a molecular microbiological approach that focuses on the identification and characterization of microbial genes involved in plant toxin metabolism, and (iii) an analytical chemical route that aims to characterize the conversion of the toxin to less harmful metabolites in vivo and link conversion to the activities of a detoxifying symbiont. The advantages and challenges of each approach are discussed, and it is argued that a multi-pronged strategy combining phenotypic, molecular, and chemical evidence is needed to unambiguously demonstrate microbial contributions to plant toxin reduction and the importance of these processes for host fitness. Given the interdisciplinary nature of the topic, we aim to provide a guideline to researchers interested in symbiont-mediated detoxification and hope to encourage future studies that contribute to a more comprehensive and mechanistic understanding of detoxification in herbivores and their symbionts.

Metabolic Enabling and Detoxification by Mammalian Gut Microbes

The longstanding interactions between mammals and their symbionts enable thousands of mammal species to consume herbivorous diets. The microbial communities in mammals degrade both plant fiber and toxins. Microbial toxin degradation has been repeatedly documented in domestic ruminants, but similar work in wild mammals is more limited due to constraints on sampling and manipulating the microbial communities in these species. In this review, we briefly describe the toxins commonly encountered in mammalian diets, major classes of biotransformation enzymes in microbes and mammals, and the gut chambers that house symbiotic microbes. We next examine evidence for microbial detoxification in domestic ruminants before providing case studies on microbial toxin degradation in both foregut- and hindgut-fermenting wild mammals. We end by discussing species that may be promising for future investigations, and the advantages and limitations of approaches currently available for studying degradation of toxins by mammalian gut microbes. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Performance, Rumen Microbial Community and Immune Status of Goat Kids Fed Leucaena leucocephala Post-weaning as Affected by Prenatal and Early Life Nutritional Interventions

Leucaena leucocephala represents a local protein source in tropical ruminant diets. However, its full exploitation is impaired by mimosine, unless it is degraded by the rumen microbial community. Recently, the ruminal bacterial communities of newborns were persistently modified through prenatal or postnatal dietary interventions. Such early-life interventions might enhance adaptation of ruminants to Leucaena leucocephala, which was investigated using a 2 × 2 factorial design trial that tested both supplementation of L. leucocephala in the late pregnancy diet of goat does, and supplementation of live yeast to their newborns. The composition of ruminal bacteria, immune status, as well as organic matter digestibility (OMD) and performance of kids were studied during and after the intervention. Ten pregnant goats were divided into two groups: the D+ and D- groups, which either received or did not receive 30 g of L. leucocephala forage meal during the last 7 ± 0.5 weeks of gestation. Twins from each goat were divided into the K+ and K- group (supplemented with or without 0.2 g/d of live yeast from day 3 until weaning at 8 weeks). Rumen samples were collected from 4-, 8-, 14-, and 20-weeks old kids to assess the bacterial community, while immune parameters (white blood cells, immunoglobulin M and G, and chitotriosidase activity) were measured in blood and saliva sampled at 4-, 8-, and 20-weeks. We found a stimulatory effect of the prenatal exposure on the post-weaning dry matter intake of the L. leucocephala supplemented diet, resulting in a higher daily gain and final body weight at 20 weeks in the D+ vs. D- group (406 vs. 370 g DM/d, 85.4 vs. 78.6 g/d, and 15.2 vs. 13.8 kg, respectively). Moreover, Ruminococcus represented a greater proportion of the rumen bacterial community of the D+ vs. D- kids (5.1 vs. 1.6%). Differences in the immune status were relatively small and not thought to be a driving factor of differences in animal performance. Furthermore, postnatal supplementation of live yeast favored maturation of the rumen bacterial community (i.e., greater abundance of Bacteroidetes, in particular Prevotella, and reduced abundance of Firmicutes) and protozoa colonization. Concomitantly, OMD was enhanced post-weaning, suggesting effects of the early-life intervention persisted and could have affected animal performance.

Toxin Degradation by Rumen Microorganisms: A Review

Animal feeds may contain exogenous compounds that can induce toxicity when ruminants ingest them. These toxins are secondary metabolites originating from various sources including plants, bacteria, algae and fungi. Animal feed toxins are responsible for various animal poisonings which negatively impact the livestock industry. Poisoning is more frequently reported in newly exposed, naïve ruminants while ‘experienced’ ruminants are observed to better tolerate toxin-contaminated feed. Ruminants can possess detoxification ability through rumen microorganisms with the rumen microbiome able to adapt to utilise toxic secondary metabolites. The ability of rumen microorganisms to metabolise these toxins has been used as a basis for the development of preventative probiotics to confer resistance against the poisoning to naïve ruminants. In this review, detoxification of various toxins, which include plant toxins, cyanobacteria toxins and plant-associated fungal mycotoxins, by rumen microorganisms is discussed. The review will include clinical studies of the animal poisoning caused by these toxins, the toxin mechanism of action, toxin degradation by rumen microorganisms, reported and hypothesised detoxification mechanisms and identified toxin metabolites with their toxicity compared to their parent toxin. This review highlights the commercial potential of rumen inoculum derived probiotics as viable means of improving ruminant health and production.

Plant secondary metabolites induced electron flux in microbial fuel cell: investigation from laboratory-to-field scale

Wastewater treatment coupled with electricity recovery in microbial fuel cell (MFC) prefer mixed anaerobic sludge as inoculum in anodic chamber than pure stain of electroactive bacteria (EAB), due to robustness and syntrophic association. Genetic modification is difficult to adopt for mixed sludge microbes for enhancing power production of MFC. Hence, we demonstrated use of eco-friendly plant secondary metabolites (PSM) with sub-lethal concentrations to enhance the rate of extracellular electron transfer between EAB and anode and validated it in both bench-scale as well as pilot-scale MFCs. The PSMs contain tannin, saponin and essential oils, which are having electron shuttling properties and their addition to microbes can cause alteration in cell morphology, electroactive behaviour and shifting in microbial population dynamics depending upon concentrations and types of PSM used. Improvement of 2.1-times and 3.8-times in power densities was observed in two different MFCs inoculated with Eucalyptus-extract pre-treated mixed anaerobic sludge and pure culture of Pseudomonas aeruginosa, respectively, as compared to respective control MFCs operated without adding Eucalyptus-extract to inoculum. When Eucalyptus-extract-dose was spiked to anodic chamber (125 l) of pilot-scale MFC, treating septage, the current production was dramatically improved. Thus, PSM-dosing to inoculum holds exciting promise for increasing electricity production of field-scale MFCs.

Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koala

Background

Differences between individuals in their gastrointestinal microbiomes can lead to variation in their ability to persist on particular diets. Koalas are dietary specialists, feeding almost exclusively on Eucalyptus foliage but many individuals will not feed on particular Eucalyptus species that are adequate food for other individuals, even when facing starvation. We undertook a faecal inoculation experiment to test whether a koala’s gastrointestinal (GI) microbiome influences their diet. Wild-caught koalas that initially fed on the preferred manna gum (Eucalyptus viminalis) were brought into captivity and orally inoculated with encapsulated material derived from faeces from koalas feeding on either the less preferred messmate (E. obliqua; treatment) or manna gum (control).

Results

The gastrointestinal microbiomes of wild koalas feeding primarily on manna gum were distinct from those feeding primarily on messmate. We found that the gastrointestinal microbiomes of koalas were unresponsive to dietary changes because the control koalas’ GI microbiomes did not change even when the nocturnal koalas were fed exclusively on messmate overnight. We showed that faecal inoculations can assist the GI microbiomes of koalas to change as the treatment koalas’ GI microbiomes became more similar to those of wild koalas feeding on messmate. There was no overall difference between the control and treatment koalas in the quantity of messmate they consumed. However, the greater the change in the koalas’ GI microbiomes, the more messmate they consumed after the inoculations had established.

Conclusions

The results suggest that dietary changes can only lead to changes in the GI microbiomes of koalas if the appropriate microbial species are present, and/or that the koala gastrointestinal microbiome influences diet selection.

Electronic supplementary material

The online version of this article (10.1186/s42523-019-0008-0) contains supplementary material, which is available to authorized users.

Metagenomic sequencing provides insights into microbial detoxification in the guts of small mammalian herbivores (Neotoma spp.)

Microbial detoxification of plant toxins influences the use of plants as food sources by herbivores. Stephen's woodrats (Neotoma stephensi) specialize on juniper, which is defended by oxalate, phenolics and monoterpenes, while closely related N. albigula specialize on cactus, which only contains oxalate. Woodrats maintain two gut chambers harboring dense microbial communities: a foregut chamber proximal to the major site of toxin absorption, and a cecal chamber in their hindgut. We performed several experiments to investigate the location and nature of microbial detoxification in the woodrat gut. First, we measured toxin concentrations across gut chambers of N. stephensi. Compared to food material, oxalate concentrations were immediately lower in the foregut, while concentrations of terpenes remained high in the foregut, and were lowest in the cecal chamber. We conducted metagenomic sequencing of the foregut chambers of both woodrat species and cecal chambers of N. stephensi to compare microbial functions. We found that most genes associated with detoxification were more abundant in the cecal chambers of N. stephensi. However, some genes associated with degradation of oxalate and phenolic compounds were more abundant in the foregut chambers. Thus, microbial detoxification may take place in various chambers depending on the class of chemical compound.